Starting phenix.real_space_refine on Thu Sep 18 04:35:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rtb_19485/09_2025/8rtb_19485.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rtb_19485/09_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_19485/09_2025/8rtb_19485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rtb_19485/09_2025/8rtb_19485.map" model { file = "/net/cci-nas-00/data/ceres_data/8rtb_19485/09_2025/8rtb_19485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rtb_19485/09_2025/8rtb_19485.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 2, 'GLU:plan': 1} 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: {'ASP:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} 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: {'ARG:plan': 4, 'GLU:plan': 2, '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: {'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 4.06, per 1000 atoms: 0.29 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: 1.47 Conformation dependent library (CDL) restraints added in 683.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.57 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: 2.80 Time building geometry restraints manager: 1.91 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: 14.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.120 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.930 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG B 69 TYR 0.043 0.002 TYR H 64 PHE 0.034 0.002 PHE A 520 TRP 0.036 0.002 TRP C 50 HIS 0.008 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00561 (14467) covalent geometry : angle 0.78948 (19611) hydrogen bonds : bond 0.15150 ( 703) hydrogen bonds : angle 6.62726 ( 2004) *********************** 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 : 0.662 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: A 64 LEU cc_start: 0.6817 (tp) cc_final: 0.6609 (tp) REVERT: A 322 VAL cc_start: 0.7554 (t) cc_final: 0.7281 (t) REVERT: B 260 LEU cc_start: 0.7453 (pt) cc_final: 0.7141 (pp) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.1318 time to fit residues: 64.5707 Evaluate side-chains 220 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 320 HIS ** 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 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 = 0.3282 r_free = 0.3282 target = 0.061067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.048977 restraints weight = 78501.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.050509 restraints weight = 44904.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.051578 restraints weight = 30796.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.052311 restraints weight = 23522.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.052832 restraints weight = 19409.035| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14467 Z= 0.198 Angle : 0.715 11.403 19611 Z= 0.368 Chirality : 0.043 0.225 2148 Planarity : 0.006 0.086 2531 Dihedral : 5.109 26.420 1953 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.19 % Allowed : 10.84 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.20), residues: 1774 helix: 0.85 (0.18), residues: 861 sheet: -2.39 (0.31), residues: 269 loop : -1.77 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 85 TYR 0.033 0.002 TYR D 18 PHE 0.026 0.002 PHE B 391 TRP 0.019 0.002 TRP C 50 HIS 0.009 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00425 (14467) covalent geometry : angle 0.71475 (19611) hydrogen bonds : bond 0.04699 ( 703) hydrogen bonds : angle 5.35553 ( 2004) *********************** 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 279 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 247 time to evaluate : 0.575 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 101 ARG cc_start: 0.8275 (pmt170) cc_final: 0.7790 (pmt170) REVERT: A 18 GLN cc_start: 0.8867 (mp10) cc_final: 0.8637 (mp10) REVERT: A 216 ASP cc_start: 0.9177 (m-30) cc_final: 0.8902 (p0) REVERT: A 245 MET cc_start: 0.8959 (ttm) cc_final: 0.8654 (ttm) REVERT: A 311 GLU cc_start: 0.9499 (tt0) cc_final: 0.9281 (tp30) REVERT: A 323 MET cc_start: 0.8572 (mmm) cc_final: 0.8244 (mmm) REVERT: A 449 LEU cc_start: 0.9605 (mp) cc_final: 0.9238 (pp) REVERT: A 465 LEU cc_start: 0.9684 (mt) cc_final: 0.9469 (pp) REVERT: A 527 LYS cc_start: 0.9690 (tppt) cc_final: 0.9481 (ttpt) REVERT: A 634 MET cc_start: 0.9571 (ttt) cc_final: 0.9286 (ttt) REVERT: A 650 MET cc_start: 0.9518 (mtp) cc_final: 0.8982 (mmm) REVERT: A 771 GLU cc_start: 0.9277 (mt-10) cc_final: 0.9007 (mp0) REVERT: B 62 ARG cc_start: 0.9485 (mtt180) cc_final: 0.9241 (mtm-85) REVERT: B 80 THR cc_start: 0.9587 (m) cc_final: 0.9336 (p) REVERT: B 199 LEU cc_start: 0.9774 (tp) cc_final: 0.9502 (tp) REVERT: B 643 MET cc_start: 0.8831 (tmm) cc_final: 0.8622 (ppp) REVERT: B 650 MET cc_start: 0.9295 (ttm) cc_final: 0.9042 (ttm) REVERT: B 759 MET cc_start: 0.8970 (tmm) cc_final: 0.8648 (tmm) REVERT: E 20 GLU cc_start: 0.9413 (mm-30) cc_final: 0.9150 (mm-30) REVERT: E 49 PHE cc_start: 0.9492 (t80) cc_final: 0.9152 (t80) REVERT: D 19 GLU cc_start: 0.9550 (tm-30) cc_final: 0.9305 (pp20) REVERT: D 20 GLU cc_start: 0.9014 (pp20) cc_final: 0.8786 (pp20) REVERT: D 49 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.8209 (t80) REVERT: J 40 LEU cc_start: 0.9616 (tp) cc_final: 0.9335 (tp) REVERT: J 63 PHE cc_start: 0.8663 (m-80) cc_final: 0.7751 (m-80) outliers start: 32 outliers final: 15 residues processed: 265 average time/residue: 0.1222 time to fit residues: 48.9067 Evaluate side-chains 241 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 225 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 172 LYS 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 718 ASP Chi-restraints excluded: chain B residue 125 VAL 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 G residue 61 PHE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 67 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 175 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN A 704 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 = 0.3270 r_free = 0.3270 target = 0.059977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.047971 restraints weight = 80326.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.049494 restraints weight = 46056.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.050547 restraints weight = 31535.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.051290 restraints weight = 24074.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.051803 restraints weight = 19819.424| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14467 Z= 0.184 Angle : 0.655 9.632 19611 Z= 0.335 Chirality : 0.042 0.225 2148 Planarity : 0.005 0.054 2531 Dihedral : 4.783 26.430 1953 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.88 % Allowed : 13.44 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.20), residues: 1774 helix: 1.00 (0.18), residues: 864 sheet: -2.11 (0.33), residues: 248 loop : -1.57 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 242 TYR 0.046 0.002 TYR D 18 PHE 0.026 0.002 PHE J 44 TRP 0.021 0.001 TRP A 657 HIS 0.007 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00393 (14467) covalent geometry : angle 0.65517 (19611) hydrogen bonds : bond 0.04239 ( 703) hydrogen bonds : angle 5.07620 ( 2004) *********************** 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 273 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 0.594 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 32 MET cc_start: 0.9374 (tpp) cc_final: 0.8993 (tpp) REVERT: C 68 ASP cc_start: 0.8333 (m-30) cc_final: 0.8048 (t0) REVERT: C 69 LYS cc_start: 0.9103 (mtpt) cc_final: 0.8874 (mtmt) REVERT: C 84 ASN cc_start: 0.9214 (t0) cc_final: 0.8958 (t0) REVERT: C 100 TYR cc_start: 0.8333 (m-80) cc_final: 0.8113 (m-10) REVERT: C 101 ARG cc_start: 0.8218 (pmt170) cc_final: 0.7773 (pmt170) REVERT: A 216 ASP cc_start: 0.9197 (m-30) cc_final: 0.8870 (p0) REVERT: A 218 MET cc_start: 0.9344 (ttt) cc_final: 0.8928 (tpp) REVERT: A 245 MET cc_start: 0.9051 (ttm) cc_final: 0.8749 (ttm) REVERT: A 295 LEU cc_start: 0.9628 (tp) cc_final: 0.8910 (tp) REVERT: A 305 GLN cc_start: 0.8806 (tp40) cc_final: 0.7989 (tp40) REVERT: A 311 GLU cc_start: 0.9513 (tt0) cc_final: 0.9304 (tp30) REVERT: A 323 MET cc_start: 0.8491 (mmm) cc_final: 0.8141 (mmm) REVERT: A 401 MET cc_start: 0.8041 (ttp) cc_final: 0.7462 (mtp) REVERT: A 448 MET cc_start: 0.8960 (tpt) cc_final: 0.8594 (tpt) REVERT: A 465 LEU cc_start: 0.9675 (mt) cc_final: 0.9445 (pp) REVERT: A 484 MET cc_start: 0.9612 (mtp) cc_final: 0.9299 (ptp) REVERT: A 527 LYS cc_start: 0.9681 (tppt) cc_final: 0.9464 (ttpt) REVERT: A 634 MET cc_start: 0.9581 (ttt) cc_final: 0.9187 (ttt) REVERT: A 650 MET cc_start: 0.9522 (mtp) cc_final: 0.8998 (mmm) REVERT: A 719 TYR cc_start: 0.9569 (t80) cc_final: 0.9355 (t80) REVERT: B 62 ARG cc_start: 0.9487 (mtt180) cc_final: 0.9228 (mtm-85) REVERT: B 68 LEU cc_start: 0.9808 (tp) cc_final: 0.9462 (pp) REVERT: B 80 THR cc_start: 0.9627 (m) cc_final: 0.9325 (p) REVERT: B 199 LEU cc_start: 0.9783 (tp) cc_final: 0.9542 (tp) REVERT: B 759 MET cc_start: 0.8951 (tmm) cc_final: 0.8747 (tmm) REVERT: E 26 ARG cc_start: 0.9081 (ttp80) cc_final: 0.8737 (ttp80) REVERT: E 31 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8668 (pp20) REVERT: J 58 MET cc_start: 0.9103 (mpp) cc_final: 0.8528 (pmm) REVERT: J 63 PHE cc_start: 0.8758 (m-80) cc_final: 0.7753 (m-80) outliers start: 42 outliers final: 22 residues processed: 256 average time/residue: 0.1187 time to fit residues: 45.8612 Evaluate side-chains 237 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 65 ASN Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain B residue 332 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 84 optimal weight: 0.0030 chunk 116 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.5998 ------------------------------------------------------------------------------- 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 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.059400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.047628 restraints weight = 80103.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.049138 restraints weight = 45320.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.050189 restraints weight = 30871.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.050927 restraints weight = 23501.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.051453 restraints weight = 19285.568| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14467 Z= 0.172 Angle : 0.639 8.374 19611 Z= 0.326 Chirality : 0.042 0.244 2148 Planarity : 0.004 0.043 2531 Dihedral : 4.630 25.879 1953 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.95 % Allowed : 16.60 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.20), residues: 1774 helix: 1.15 (0.18), residues: 858 sheet: -1.94 (0.33), residues: 255 loop : -1.40 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 72 TYR 0.027 0.002 TYR H 28 PHE 0.036 0.001 PHE J 44 TRP 0.017 0.001 TRP A 808 HIS 0.006 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00371 (14467) covalent geometry : angle 0.63933 (19611) hydrogen bonds : bond 0.04007 ( 703) hydrogen bonds : angle 4.90526 ( 2004) *********************** 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 259 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 time to evaluate : 0.606 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 68 ASP cc_start: 0.8333 (m-30) cc_final: 0.8088 (t70) REVERT: C 84 ASN cc_start: 0.9238 (t0) cc_final: 0.8978 (t0) REVERT: A 216 ASP cc_start: 0.9183 (m-30) cc_final: 0.8883 (p0) REVERT: A 218 MET cc_start: 0.9320 (ttt) cc_final: 0.8967 (tpp) REVERT: A 323 MET cc_start: 0.8371 (mmm) cc_final: 0.8111 (mmm) REVERT: A 401 MET cc_start: 0.8166 (ttp) cc_final: 0.7515 (mtp) REVERT: A 448 MET cc_start: 0.8982 (tpt) cc_final: 0.8637 (tpt) REVERT: A 465 LEU cc_start: 0.9666 (mt) cc_final: 0.9457 (pp) REVERT: A 484 MET cc_start: 0.9602 (mtp) cc_final: 0.9330 (ptp) REVERT: A 634 MET cc_start: 0.9557 (ttt) cc_final: 0.8909 (ttt) REVERT: A 650 MET cc_start: 0.9490 (mtp) cc_final: 0.8952 (mmm) REVERT: B 62 ARG cc_start: 0.9467 (mtt180) cc_final: 0.9208 (mtm-85) REVERT: B 80 THR cc_start: 0.9599 (m) cc_final: 0.9336 (p) REVERT: B 218 MET cc_start: 0.9092 (ttm) cc_final: 0.8891 (ttm) REVERT: B 448 MET cc_start: 0.8307 (mtt) cc_final: 0.8096 (mtt) REVERT: B 643 MET cc_start: 0.8790 (tmm) cc_final: 0.8513 (ppp) REVERT: B 759 MET cc_start: 0.8954 (tmm) cc_final: 0.8665 (tmm) REVERT: E 14 LEU cc_start: 0.9536 (mt) cc_final: 0.9114 (tt) REVERT: E 26 ARG cc_start: 0.9005 (ttp80) cc_final: 0.8759 (ttp80) REVERT: G 54 MET cc_start: 0.6660 (tpt) cc_final: 0.6319 (tpt) REVERT: J 58 MET cc_start: 0.9069 (mpp) cc_final: 0.8527 (pmm) REVERT: J 63 PHE cc_start: 0.8757 (m-80) cc_final: 0.7727 (m-80) outliers start: 43 outliers final: 29 residues processed: 243 average time/residue: 0.1211 time to fit residues: 44.2427 Evaluate side-chains 231 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 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 172 LYS 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 460 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 246 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 E residue 18 TYR 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 58 VAL Chi-restraints excluded: chain H residue 59 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 130 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 71 optimal weight: 0.4980 chunk 134 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** 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 = 0.3286 r_free = 0.3286 target = 0.060091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.048451 restraints weight = 79031.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.049984 restraints weight = 44486.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.051054 restraints weight = 30101.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.051793 restraints weight = 22809.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.052322 restraints weight = 18681.841| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14467 Z= 0.132 Angle : 0.625 11.463 19611 Z= 0.313 Chirality : 0.043 0.375 2148 Planarity : 0.004 0.042 2531 Dihedral : 4.481 23.419 1953 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.02 % Allowed : 17.90 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.20), residues: 1774 helix: 1.23 (0.18), residues: 865 sheet: -1.65 (0.33), residues: 255 loop : -1.37 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 103 TYR 0.026 0.001 TYR H 28 PHE 0.036 0.001 PHE J 44 TRP 0.018 0.001 TRP A 808 HIS 0.006 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00299 (14467) covalent geometry : angle 0.62498 (19611) hydrogen bonds : bond 0.03737 ( 703) hydrogen bonds : angle 4.67338 ( 2004) *********************** 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 269 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 0.629 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 68 ASP cc_start: 0.8307 (m-30) cc_final: 0.7990 (t70) REVERT: C 69 LYS cc_start: 0.9293 (mtmm) cc_final: 0.9047 (ptpt) REVERT: C 84 ASN cc_start: 0.9219 (t0) cc_final: 0.8934 (t0) REVERT: A 20 ILE cc_start: 0.9681 (mt) cc_final: 0.9338 (tp) REVERT: A 216 ASP cc_start: 0.9175 (m-30) cc_final: 0.8876 (p0) REVERT: A 218 MET cc_start: 0.9250 (ttt) cc_final: 0.8626 (tpt) REVERT: A 325 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8720 (mp0) REVERT: A 363 LEU cc_start: 0.9349 (tp) cc_final: 0.9064 (tp) REVERT: A 448 MET cc_start: 0.9003 (tpt) cc_final: 0.8638 (tpt) REVERT: A 465 LEU cc_start: 0.9659 (mt) cc_final: 0.9438 (pp) REVERT: A 484 MET cc_start: 0.9598 (mtp) cc_final: 0.9328 (ptp) REVERT: A 650 MET cc_start: 0.9478 (mtp) cc_final: 0.8926 (mmm) REVERT: B 62 ARG cc_start: 0.9458 (mtt180) cc_final: 0.9225 (mtm-85) REVERT: B 68 LEU cc_start: 0.9782 (tp) cc_final: 0.9463 (pp) REVERT: B 80 THR cc_start: 0.9612 (m) cc_final: 0.9346 (p) REVERT: B 199 LEU cc_start: 0.9781 (tp) cc_final: 0.9531 (tt) REVERT: B 207 MET cc_start: 0.7977 (pmm) cc_final: 0.7587 (pmm) REVERT: B 448 MET cc_start: 0.8382 (mtt) cc_final: 0.8069 (mtt) REVERT: B 759 MET cc_start: 0.8925 (tmm) cc_final: 0.8572 (tmm) REVERT: E 14 LEU cc_start: 0.9448 (mt) cc_final: 0.9114 (tt) REVERT: E 26 ARG cc_start: 0.8969 (ttp80) cc_final: 0.8743 (ttp80) REVERT: F 31 GLU cc_start: 0.9079 (tp30) cc_final: 0.8854 (tp30) outliers start: 44 outliers final: 27 residues processed: 253 average time/residue: 0.1233 time to fit residues: 46.6561 Evaluate side-chains 230 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 246 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 130 optimal weight: 0.0170 chunk 89 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 142 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 99 optimal weight: 0.3980 chunk 84 optimal weight: 0.0040 overall best weight: 0.3030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** 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 = 0.3300 r_free = 0.3300 target = 0.060844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.049162 restraints weight = 78887.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.050737 restraints weight = 44059.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.051825 restraints weight = 29657.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.052585 restraints weight = 22355.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.053094 restraints weight = 18195.570| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3939 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= 0.121 Angle : 0.662 12.540 19611 Z= 0.325 Chirality : 0.043 0.391 2148 Planarity : 0.004 0.052 2531 Dihedral : 4.354 21.061 1953 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.61 % Allowed : 18.79 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.20), residues: 1774 helix: 1.32 (0.18), residues: 853 sheet: -1.31 (0.34), residues: 247 loop : -1.21 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 103 TYR 0.021 0.001 TYR H 28 PHE 0.041 0.001 PHE J 44 TRP 0.019 0.001 TRP A 808 HIS 0.006 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00277 (14467) covalent geometry : angle 0.66194 (19611) hydrogen bonds : bond 0.03655 ( 703) hydrogen bonds : angle 4.55180 ( 2004) *********************** 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 264 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 0.611 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 67 ASP cc_start: 0.8724 (m-30) cc_final: 0.8138 (m-30) REVERT: C 68 ASP cc_start: 0.8377 (m-30) cc_final: 0.7983 (t70) REVERT: C 84 ASN cc_start: 0.9174 (t0) cc_final: 0.8876 (t0) REVERT: A 10 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9162 (mt) REVERT: A 117 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8153 (ptp) REVERT: A 218 MET cc_start: 0.9129 (ttt) cc_final: 0.8919 (tpt) REVERT: A 286 GLU cc_start: 0.9330 (tm-30) cc_final: 0.9040 (tm-30) REVERT: A 325 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8791 (mp0) REVERT: A 401 MET cc_start: 0.7933 (ttp) cc_final: 0.7446 (mtp) REVERT: A 448 MET cc_start: 0.8995 (tpt) cc_final: 0.8631 (tpt) REVERT: A 465 LEU cc_start: 0.9652 (mt) cc_final: 0.9421 (pp) REVERT: A 484 MET cc_start: 0.9602 (mtp) cc_final: 0.9322 (ptp) REVERT: A 650 MET cc_start: 0.9483 (mtp) cc_final: 0.8868 (mmm) REVERT: A 692 ASP cc_start: 0.9623 (t0) cc_final: 0.9315 (t0) REVERT: B 62 ARG cc_start: 0.9455 (mtt180) cc_final: 0.9170 (mtm-85) REVERT: B 68 LEU cc_start: 0.9782 (tp) cc_final: 0.9465 (pp) REVERT: B 80 THR cc_start: 0.9615 (m) cc_final: 0.9342 (p) REVERT: B 199 LEU cc_start: 0.9773 (tp) cc_final: 0.9539 (tt) REVERT: B 207 MET cc_start: 0.8006 (pmm) cc_final: 0.7544 (pmm) REVERT: B 401 MET cc_start: 0.8883 (tmm) cc_final: 0.8390 (ptm) REVERT: B 448 MET cc_start: 0.8446 (mtt) cc_final: 0.8142 (mtt) REVERT: B 629 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.8051 (mtt-85) REVERT: B 759 MET cc_start: 0.8875 (tmm) cc_final: 0.8499 (tmm) REVERT: E 14 LEU cc_start: 0.9371 (mt) cc_final: 0.8953 (tt) REVERT: E 26 ARG cc_start: 0.8964 (ttp80) cc_final: 0.8759 (ttp80) REVERT: D 19 GLU cc_start: 0.9515 (tm-30) cc_final: 0.9264 (pp20) REVERT: D 20 GLU cc_start: 0.9117 (pp20) cc_final: 0.8831 (pp20) REVERT: J 58 MET cc_start: 0.8745 (pmm) cc_final: 0.8166 (pmm) outliers start: 38 outliers final: 25 residues processed: 251 average time/residue: 0.1220 time to fit residues: 46.0438 Evaluate side-chains 234 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 246 LEU 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 32 PHE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain H residue 28 TYR Chi-restraints excluded: chain H residue 52 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 74 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 151 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.058106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.046735 restraints weight = 81587.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.048169 restraints weight = 47125.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.049164 restraints weight = 32366.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.049868 restraints weight = 24842.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.050361 restraints weight = 20465.069| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14467 Z= 0.215 Angle : 0.691 11.062 19611 Z= 0.351 Chirality : 0.043 0.321 2148 Planarity : 0.004 0.042 2531 Dihedral : 4.449 22.442 1953 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.09 % Allowed : 19.27 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.21), residues: 1774 helix: 1.18 (0.18), residues: 860 sheet: -1.34 (0.33), residues: 270 loop : -1.17 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 103 TYR 0.032 0.002 TYR H 64 PHE 0.040 0.002 PHE J 44 TRP 0.041 0.002 TRP C 50 HIS 0.006 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00454 (14467) covalent geometry : angle 0.69067 (19611) hydrogen bonds : bond 0.03942 ( 703) hydrogen bonds : angle 4.80476 ( 2004) *********************** 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 252 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 0.606 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 67 ASP cc_start: 0.8762 (m-30) cc_final: 0.8189 (m-30) REVERT: C 68 ASP cc_start: 0.8450 (m-30) cc_final: 0.7943 (t70) REVERT: C 84 ASN cc_start: 0.9295 (t0) cc_final: 0.9003 (t0) REVERT: A 216 ASP cc_start: 0.9227 (m-30) cc_final: 0.8848 (p0) REVERT: A 325 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8753 (mp0) REVERT: A 401 MET cc_start: 0.8106 (ttp) cc_final: 0.7676 (mtp) REVERT: A 448 MET cc_start: 0.9034 (tpt) cc_final: 0.8662 (tpt) REVERT: A 449 LEU cc_start: 0.9539 (tp) cc_final: 0.9339 (tp) REVERT: A 465 LEU cc_start: 0.9674 (mt) cc_final: 0.9438 (pp) REVERT: A 484 MET cc_start: 0.9604 (mtp) cc_final: 0.9346 (ptp) REVERT: A 650 MET cc_start: 0.9452 (mtp) cc_final: 0.8824 (mmm) REVERT: A 692 ASP cc_start: 0.9621 (t0) cc_final: 0.9349 (t0) REVERT: B 62 ARG cc_start: 0.9438 (mtt180) cc_final: 0.9160 (mtm-85) REVERT: B 80 THR cc_start: 0.9608 (m) cc_final: 0.9353 (p) REVERT: B 199 LEU cc_start: 0.9791 (tp) cc_final: 0.9569 (tt) REVERT: B 448 MET cc_start: 0.8365 (mtt) cc_final: 0.8008 (mtt) REVERT: B 629 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8062 (mtt-85) REVERT: B 759 MET cc_start: 0.8959 (tmm) cc_final: 0.8571 (tmm) REVERT: E 14 LEU cc_start: 0.9263 (mt) cc_final: 0.8871 (tt) REVERT: E 22 ARG cc_start: 0.9452 (mtt180) cc_final: 0.8860 (mtt90) REVERT: D 54 MET cc_start: 0.8953 (tmm) cc_final: 0.8498 (ppp) REVERT: J 58 MET cc_start: 0.8901 (pmm) cc_final: 0.8307 (pmm) outliers start: 45 outliers final: 30 residues processed: 238 average time/residue: 0.1194 time to fit residues: 43.2082 Evaluate side-chains 225 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 718 ASP 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 246 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 29 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 55 VAL 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 11 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 172 optimal weight: 0.0770 chunk 14 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** 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 = 0.3256 r_free = 0.3256 target = 0.058449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.047125 restraints weight = 81091.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.048567 restraints weight = 46481.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.049573 restraints weight = 31848.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.050289 restraints weight = 24352.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.050777 restraints weight = 19987.972| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4314 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= 0.171 Angle : 0.691 13.994 19611 Z= 0.344 Chirality : 0.044 0.363 2148 Planarity : 0.004 0.045 2531 Dihedral : 4.401 21.369 1953 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.95 % Allowed : 20.23 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.21), residues: 1774 helix: 1.25 (0.18), residues: 855 sheet: -1.33 (0.33), residues: 267 loop : -1.06 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 103 TYR 0.023 0.002 TYR H 64 PHE 0.044 0.001 PHE J 44 TRP 0.031 0.002 TRP C 50 HIS 0.004 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00373 (14467) covalent geometry : angle 0.69120 (19611) hydrogen bonds : bond 0.03791 ( 703) hydrogen bonds : angle 4.74019 ( 2004) *********************** 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 248 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 205 time to evaluate : 0.621 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: 0.9267 (t0) cc_final: 0.8943 (t0) REVERT: A 117 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.7912 (ptp) REVERT: A 216 ASP cc_start: 0.9230 (m-30) cc_final: 0.8879 (p0) REVERT: A 325 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8767 (mp0) REVERT: A 401 MET cc_start: 0.8166 (ttp) cc_final: 0.7752 (mtp) REVERT: A 448 MET cc_start: 0.9040 (tpt) cc_final: 0.8501 (tpt) REVERT: A 449 LEU cc_start: 0.9531 (tp) cc_final: 0.9242 (tp) REVERT: A 465 LEU cc_start: 0.9669 (mt) cc_final: 0.9401 (pp) REVERT: A 650 MET cc_start: 0.9444 (mtp) cc_final: 0.8907 (mmm) REVERT: A 692 ASP cc_start: 0.9622 (t0) cc_final: 0.9315 (t0) REVERT: B 62 ARG cc_start: 0.9439 (mtt180) cc_final: 0.9205 (mtm-85) REVERT: B 80 THR cc_start: 0.9612 (m) cc_final: 0.9349 (p) REVERT: B 199 LEU cc_start: 0.9785 (tp) cc_final: 0.9570 (tt) REVERT: B 448 MET cc_start: 0.8380 (mtt) cc_final: 0.8036 (mtt) REVERT: B 629 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8120 (mtt-85) REVERT: B 759 MET cc_start: 0.8884 (tmm) cc_final: 0.8503 (tmm) REVERT: E 14 LEU cc_start: 0.9246 (mt) cc_final: 0.8838 (tt) REVERT: J 58 MET cc_start: 0.8910 (pmm) cc_final: 0.8688 (pmm) outliers start: 43 outliers final: 31 residues processed: 237 average time/residue: 0.1193 time to fit residues: 43.1136 Evaluate side-chains 231 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 718 ASP 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 246 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 55 VAL 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 20 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 95 optimal weight: 8.9990 chunk 48 optimal weight: 0.0270 chunk 28 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** 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 = 0.3255 r_free = 0.3255 target = 0.058257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.046905 restraints weight = 81183.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.048384 restraints weight = 45735.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.049418 restraints weight = 31050.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.050144 restraints weight = 23537.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.050650 restraints weight = 19245.413| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.4441 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= 0.169 Angle : 0.712 13.854 19611 Z= 0.349 Chirality : 0.044 0.339 2148 Planarity : 0.004 0.045 2531 Dihedral : 4.370 20.607 1953 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.61 % Allowed : 20.78 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.20), residues: 1774 helix: 1.23 (0.18), residues: 858 sheet: -1.22 (0.32), residues: 277 loop : -1.09 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 103 TYR 0.024 0.002 TYR H 64 PHE 0.047 0.001 PHE J 44 TRP 0.041 0.002 TRP C 50 HIS 0.004 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00370 (14467) covalent geometry : angle 0.71218 (19611) hydrogen bonds : bond 0.03810 ( 703) hydrogen bonds : angle 4.73191 ( 2004) *********************** 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 241 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 ASP cc_start: 0.8238 (m-30) cc_final: 0.7673 (t0) REVERT: C 69 LYS cc_start: 0.9214 (ptpp) cc_final: 0.8996 (ptpp) REVERT: C 84 ASN cc_start: 0.9261 (t0) cc_final: 0.8928 (t0) REVERT: A 117 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.7781 (ptp) REVERT: A 216 ASP cc_start: 0.9226 (m-30) cc_final: 0.8881 (p0) REVERT: A 325 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8659 (mp0) REVERT: A 401 MET cc_start: 0.7799 (ttp) cc_final: 0.7443 (mtp) REVERT: A 448 MET cc_start: 0.9016 (tpt) cc_final: 0.8461 (tpt) REVERT: A 449 LEU cc_start: 0.9522 (tp) cc_final: 0.9233 (tp) REVERT: A 465 LEU cc_start: 0.9675 (mt) cc_final: 0.9382 (pp) REVERT: A 484 MET cc_start: 0.9653 (mtp) cc_final: 0.9423 (ptp) REVERT: A 650 MET cc_start: 0.9470 (mtp) cc_final: 0.8887 (mmm) REVERT: A 692 ASP cc_start: 0.9621 (t0) cc_final: 0.9320 (t0) REVERT: B 62 ARG cc_start: 0.9435 (mtt180) cc_final: 0.9154 (mtm-85) REVERT: B 80 THR cc_start: 0.9625 (m) cc_final: 0.9373 (p) REVERT: B 199 LEU cc_start: 0.9807 (tp) cc_final: 0.9566 (tt) REVERT: B 448 MET cc_start: 0.8367 (mtt) cc_final: 0.8011 (mtt) REVERT: B 629 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8009 (mtt180) REVERT: B 759 MET cc_start: 0.8870 (tmm) cc_final: 0.8510 (tmm) REVERT: E 14 LEU cc_start: 0.9303 (mt) cc_final: 0.8873 (tt) REVERT: E 61 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7446 (m-80) REVERT: D 19 GLU cc_start: 0.9492 (tm-30) cc_final: 0.9250 (pp20) REVERT: D 20 GLU cc_start: 0.9041 (pp20) cc_final: 0.8838 (pp20) REVERT: D 54 MET cc_start: 0.9056 (tmm) cc_final: 0.8541 (ppp) REVERT: G 54 MET cc_start: 0.7269 (ppp) cc_final: 0.6978 (ppp) REVERT: J 58 MET cc_start: 0.8972 (pmm) cc_final: 0.8734 (pmm) outliers start: 38 outliers final: 31 residues processed: 230 average time/residue: 0.1204 time to fit residues: 42.1788 Evaluate side-chains 233 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 718 ASP 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 246 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 55 VAL 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 Chi-restraints excluded: chain H residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 32 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 170 optimal weight: 0.9990 chunk 70 optimal weight: 0.2980 chunk 75 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN A 428 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.059172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.047860 restraints weight = 80842.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.049350 restraints weight = 46202.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.050362 restraints weight = 31561.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.051097 restraints weight = 24059.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.051619 restraints weight = 19730.851| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14467 Z= 0.129 Angle : 0.727 14.958 19611 Z= 0.348 Chirality : 0.045 0.388 2148 Planarity : 0.004 0.052 2531 Dihedral : 4.283 19.502 1953 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.26 % Allowed : 21.67 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.21), residues: 1774 helix: 1.33 (0.18), residues: 847 sheet: -0.97 (0.34), residues: 260 loop : -0.96 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 103 TYR 0.020 0.001 TYR A 719 PHE 0.048 0.001 PHE J 44 TRP 0.040 0.002 TRP C 50 HIS 0.004 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00299 (14467) covalent geometry : angle 0.72739 (19611) hydrogen bonds : bond 0.03623 ( 703) hydrogen bonds : angle 4.72203 ( 2004) ********************** 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 250 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 217 time to evaluate : 0.597 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 67 ASP cc_start: 0.8887 (m-30) cc_final: 0.8488 (t70) REVERT: C 84 ASN cc_start: 0.9216 (t0) cc_final: 0.8865 (t0) REVERT: A 216 ASP cc_start: 0.9185 (m-30) cc_final: 0.8812 (p0) REVERT: A 286 GLU cc_start: 0.9309 (tm-30) cc_final: 0.9001 (tm-30) REVERT: A 325 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8654 (mp0) REVERT: A 401 MET cc_start: 0.7829 (ttp) cc_final: 0.7300 (mtp) REVERT: A 448 MET cc_start: 0.9044 (tpt) cc_final: 0.8487 (tpt) REVERT: A 465 LEU cc_start: 0.9657 (mt) cc_final: 0.9380 (pp) REVERT: A 484 MET cc_start: 0.9665 (mtp) cc_final: 0.9429 (ptp) REVERT: A 650 MET cc_start: 0.9449 (mtp) cc_final: 0.8836 (mmm) REVERT: A 692 ASP cc_start: 0.9584 (t0) cc_final: 0.9189 (t0) REVERT: B 62 ARG cc_start: 0.9417 (mtt180) cc_final: 0.9164 (mtm-85) REVERT: B 80 THR cc_start: 0.9590 (m) cc_final: 0.9342 (p) REVERT: B 629 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7990 (mtt180) REVERT: B 759 MET cc_start: 0.8845 (tmm) cc_final: 0.8493 (tmm) REVERT: E 14 LEU cc_start: 0.9291 (mt) cc_final: 0.8867 (tt) REVERT: E 61 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: D 54 MET cc_start: 0.9017 (tmm) cc_final: 0.8541 (ppp) REVERT: G 54 MET cc_start: 0.7254 (ppp) cc_final: 0.6889 (ppp) REVERT: J 58 MET cc_start: 0.9009 (pmm) cc_final: 0.8462 (pmm) REVERT: J 63 PHE cc_start: 0.8766 (m-80) cc_final: 0.7832 (m-80) outliers start: 33 outliers final: 27 residues processed: 241 average time/residue: 0.1225 time to fit residues: 44.2487 Evaluate side-chains 237 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 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 633 MET Chi-restraints excluded: chain A residue 718 ASP 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 246 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 D residue 51 LEU Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain F residue 55 VAL 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 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 71 optimal weight: 0.0670 chunk 117 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.057893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.046638 restraints weight = 82052.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.048113 restraints weight = 46331.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.049130 restraints weight = 31403.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.049819 restraints weight = 23807.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.050338 restraints weight = 19553.016| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4655 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= 0.186 Angle : 0.737 14.693 19611 Z= 0.362 Chirality : 0.045 0.339 2148 Planarity : 0.004 0.050 2531 Dihedral : 4.319 20.341 1953 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.26 % Allowed : 22.50 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.21), residues: 1774 helix: 1.27 (0.18), residues: 852 sheet: -0.95 (0.33), residues: 271 loop : -1.03 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 103 TYR 0.025 0.002 TYR H 64 PHE 0.050 0.001 PHE J 44 TRP 0.040 0.002 TRP C 50 HIS 0.005 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00403 (14467) covalent geometry : angle 0.73728 (19611) hydrogen bonds : bond 0.03766 ( 703) hydrogen bonds : angle 4.83291 ( 2004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3082.63 seconds wall clock time: 54 minutes 9.02 seconds (3249.02 seconds total)