Starting phenix.real_space_refine on Wed Jul 30 20:35:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oiu_12933/07_2025/7oiu_12933.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oiu_12933/07_2025/7oiu_12933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oiu_12933/07_2025/7oiu_12933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oiu_12933/07_2025/7oiu_12933.map" model { file = "/net/cci-nas-00/data/ceres_data/7oiu_12933/07_2025/7oiu_12933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oiu_12933/07_2025/7oiu_12933.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.653 sd= 4.053 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 43 5.16 5 C 8174 2.51 5 N 2197 2.21 5 O 2330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12744 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 776 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 94} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 2, 'TRP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 5701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5701 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 35, 'TRANS': 716} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 359 Unresolved non-hydrogen angles: 445 Unresolved non-hydrogen dihedrals: 293 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 14, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 228 Chain: "B" Number of atoms: 5318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5318 Classifications: {'peptide': 685} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 31, 'TRANS': 653} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 8, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 127 Chain: "D" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 346 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 49} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 355 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 248 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 40} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 7.25, per 1000 atoms: 0.57 Number of scatterers: 12744 At special positions: 0 Unit cell: (137.643, 92.829, 161.117, 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 43 16.00 O 2330 8.00 N 2197 7.00 C 8174 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: 2.93 Conformation dependent library (CDL) restraints added in 1.6 seconds 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3152 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 13 sheets defined 50.0% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'C' and resid 27 through 45 removed outlier: 3.518A pdb=" N THR C 44 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 67 removed outlier: 3.561A pdb=" N LEU C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 81 removed outlier: 3.995A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 15 through 20 removed outlier: 3.997A pdb=" N GLN A 18 " --> pdb=" O PRO A 15 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 20 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 72 removed outlier: 3.631A pdb=" N PHE A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY A 70 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 4.375A 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 134 through 141 removed outlier: 3.550A pdb=" N PHE A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 141 " --> pdb=" O PHE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 171 Processing helix chain 'A' and resid 191 through 202 removed outlier: 3.607A pdb=" N PHE A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 280 through 297 Processing helix chain 'A' and resid 303 through 319 removed outlier: 4.105A pdb=" N GLU A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ALA A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 354 removed outlier: 3.795A pdb=" N VAL A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'A' and resid 484 through 491 removed outlier: 3.526A pdb=" N MET A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 528 removed outlier: 4.060A pdb=" N LYS A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 553 removed outlier: 3.964A pdb=" N MET A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 590 removed outlier: 3.816A pdb=" N ARG A 586 " --> pdb=" O THR A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 645 Proline residue: A 631 - end of helix removed outlier: 4.181A pdb=" N SER A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N MET A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASP A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 664 through 679 removed outlier: 4.617A pdb=" N ASN A 671 " --> pdb=" O ASP A 667 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYS A 674 " --> pdb=" O LYS A 670 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 679 " --> pdb=" O THR A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 694 removed outlier: 3.925A pdb=" N LEU A 694 " --> pdb=" O PRO A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 706 removed outlier: 3.670A pdb=" N LYS A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 Processing helix chain 'A' and resid 729 through 739 Processing helix chain 'A' and resid 777 through 785 removed outlier: 4.403A pdb=" N LEU A 782 " --> pdb=" O ASP A 778 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 785 " --> pdb=" O LEU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 802 Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 808 through 820 removed outlier: 4.012A pdb=" N PHE A 812 " --> pdb=" O TRP A 808 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG A 815 " --> pdb=" O ILE A 811 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ALA A 818 " --> pdb=" O ASP A 814 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 71 removed outlier: 3.843A pdb=" N VAL B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR B 67 " --> pdb=" O GLU B 63 " (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: 3.760A pdb=" N PHE B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 218 removed outlier: 4.303A pdb=" N TYR B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 265 removed outlier: 3.772A pdb=" N GLU B 265 " --> pdb=" O VAL B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 297 Processing helix chain 'B' and resid 302 through 319 removed outlier: 4.049A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 354 removed outlier: 3.614A pdb=" N VAL B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 388 through 395 Processing helix chain 'B' and resid 456 through 469 Processing helix chain 'B' and resid 470 through 472 No H-bonds generated for 'chain 'B' and resid 470 through 472' Processing helix chain 'B' and resid 483 through 491 removed outlier: 4.200A pdb=" N SER B 487 " --> pdb=" O GLY B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 530 Processing helix chain 'B' and resid 628 through 645 removed outlier: 4.127A pdb=" N VAL B 632 " --> pdb=" O ALA B 628 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 638 " --> pdb=" O MET B 634 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B 639 " --> pdb=" O TYR B 635 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE B 644 " --> pdb=" O THR B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 removed outlier: 3.652A pdb=" N GLN B 661 " --> pdb=" O TRP B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 679 removed outlier: 4.971A pdb=" N LYS B 674 " --> pdb=" O LYS B 670 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N THR B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 694 Processing helix chain 'B' and resid 699 through 705 Processing helix chain 'B' and resid 718 through 727 removed outlier: 3.514A pdb=" N PHE B 726 " --> pdb=" O TYR B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 740 Processing helix chain 'B' and resid 776 through 785 Processing helix chain 'B' and resid 787 through 802 removed outlier: 4.020A pdb=" N GLY B 802 " --> pdb=" O ILE B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 821 removed outlier: 3.877A pdb=" N ASP B 814 " --> pdb=" O PRO B 810 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 816 " --> pdb=" O PHE B 812 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 817 " --> pdb=" O LEU B 813 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU B 819 " --> pdb=" O ARG B 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 26 Processing helix chain 'D' and resid 27 through 62 removed outlier: 3.838A pdb=" N SER D 62 " --> pdb=" O ILE D 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 61 Processing helix chain 'F' and resid 23 through 62 removed outlier: 4.178A pdb=" N ARG F 36 " --> pdb=" O PHE F 32 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER F 62 " --> pdb=" O ILE F 58 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.683A pdb=" N ILE A 248 " --> pdb=" O CYS A 328 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N CYS A 328 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N GLU A 250 " --> pdb=" O HIS A 326 " (cutoff:3.500A) removed outlier: 11.679A pdb=" N HIS A 326 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 178 removed outlier: 3.842A pdb=" N TYR A 38 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 121 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 272 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 275 " --> pdb=" O HIS A 327 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS A 327 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 11.679A pdb=" N HIS A 326 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N GLU A 250 " --> pdb=" O HIS A 326 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N CYS A 328 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 248 " --> pdb=" O CYS A 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA4, first strand: chain 'A' and resid 181 through 184 removed outlier: 3.656A pdb=" N HIS A 187 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 425 through 427 removed outlier: 3.511A pdb=" N THR A 415 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 493 through 494 removed outlier: 6.556A pdb=" N ILE A 475 " --> pdb=" O TYR A 615 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR A 474 " --> pdb=" O MET A 650 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL A 652 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL A 476 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL A 684 " --> pdb=" O PHE A 649 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TYR A 651 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ALA A 686 " --> pdb=" O TYR A 651 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N THR A 447 " --> pdb=" O PHE A 685 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N THR A 687 " --> pdb=" O THR A 447 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU A 449 " --> pdb=" O THR A 687 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N MET A 448 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU A 712 " --> pdb=" O MET A 448 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE A 450 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR A 709 " --> pdb=" O LYS A 749 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 22 through 26 removed outlier: 3.674A pdb=" N HIS B 24 " --> pdb=" O SER B 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.876A pdb=" N LEU B 121 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU B 76 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 278 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE B 270 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 275 " --> pdb=" O HIS B 327 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS B 327 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS B 328 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY B 244 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 224 through 225 removed outlier: 3.694A pdb=" N GLY B 244 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS B 328 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 181 through 182 Processing sheet with id=AB2, first strand: chain 'B' and resid 415 through 418 removed outlier: 3.520A pdb=" N THR B 415 " --> pdb=" O PHE B 427 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 447 through 450 removed outlier: 6.098A pdb=" N MET B 448 " --> pdb=" O ILE B 710 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU B 712 " --> pdb=" O MET B 448 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE B 450 " --> pdb=" O LEU B 712 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 614 through 618 removed outlier: 5.799A pdb=" N ILE B 475 " --> pdb=" O TYR B 615 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N PHE B 617 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ALA B 477 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL B 476 " --> pdb=" O VAL B 652 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N PHE B 649 " --> pdb=" O ILE B 682 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL B 684 " --> pdb=" O PHE B 649 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR B 651 " --> pdb=" O VAL B 684 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 666 hydrogen bonds defined for protein. 1932 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.01 Time building geometry restraints manager: 3.51 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: 4177 1.34 - 1.46: 2629 1.46 - 1.58: 6161 1.58 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 13042 Sorted by residual: bond pdb=" CA ILE B 20 " pdb=" CB ILE B 20 " ideal model delta sigma weight residual 1.536 1.515 0.021 1.19e-02 7.06e+03 3.18e+00 bond pdb=" CA SER A 77 " pdb=" CB SER A 77 " ideal model delta sigma weight residual 1.533 1.509 0.023 1.65e-02 3.67e+03 2.01e+00 bond pdb=" N ILE A 82 " pdb=" CA ILE A 82 " ideal model delta sigma weight residual 1.474 1.454 0.020 1.57e-02 4.06e+03 1.61e+00 bond pdb=" N VAL B 684 " pdb=" CA VAL B 684 " ideal model delta sigma weight residual 1.474 1.455 0.020 1.57e-02 4.06e+03 1.55e+00 bond pdb=" N GLU B 502 " pdb=" CA GLU B 502 " ideal model delta sigma weight residual 1.462 1.451 0.011 9.30e-03 1.16e+04 1.44e+00 ... (remaining 13037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 17100 1.58 - 3.17: 523 3.17 - 4.75: 76 4.75 - 6.34: 18 6.34 - 7.92: 5 Bond angle restraints: 17722 Sorted by residual: angle pdb=" CA GLU B 780 " pdb=" CB GLU B 780 " pdb=" CG GLU B 780 " ideal model delta sigma weight residual 114.10 122.02 -7.92 2.00e+00 2.50e-01 1.57e+01 angle pdb=" C LEU C 13 " pdb=" N PHE C 14 " pdb=" CA PHE C 14 " ideal model delta sigma weight residual 121.54 128.06 -6.52 1.91e+00 2.74e-01 1.17e+01 angle pdb=" C THR B 27 " pdb=" CA THR B 27 " pdb=" CB THR B 27 " ideal model delta sigma weight residual 111.23 106.01 5.22 1.63e+00 3.76e-01 1.03e+01 angle pdb=" C LEU A 609 " pdb=" N SER A 610 " pdb=" CA SER A 610 " ideal model delta sigma weight residual 121.54 127.37 -5.83 1.91e+00 2.74e-01 9.33e+00 angle pdb=" C TYR B 495 " pdb=" N LEU B 496 " pdb=" CA LEU B 496 " ideal model delta sigma weight residual 123.46 119.54 3.92 1.35e+00 5.49e-01 8.41e+00 ... (remaining 17717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 6984 16.78 - 33.57: 573 33.57 - 50.35: 96 50.35 - 67.14: 12 67.14 - 83.92: 8 Dihedral angle restraints: 7673 sinusoidal: 2798 harmonic: 4875 Sorted by residual: dihedral pdb=" CA PHE B 95 " pdb=" C PHE B 95 " pdb=" N ASP B 96 " pdb=" CA ASP B 96 " ideal model delta harmonic sigma weight residual -180.00 -153.05 -26.95 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA GLU A 627 " pdb=" C GLU A 627 " pdb=" N ALA A 628 " pdb=" CA ALA A 628 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA HIS A 24 " pdb=" C HIS A 24 " pdb=" N HIS A 25 " pdb=" CA HIS A 25 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 7670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1758 0.065 - 0.130: 202 0.130 - 0.196: 7 0.196 - 0.261: 0 0.261 - 0.326: 1 Chirality restraints: 1968 Sorted by residual: 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 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA GLU B 780 " pdb=" N GLU B 780 " pdb=" C GLU B 780 " pdb=" CB GLU B 780 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CA PRO B 21 " pdb=" N PRO B 21 " pdb=" C PRO B 21 " pdb=" CB PRO B 21 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 1965 not shown) Planarity restraints: 2296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 804 " -0.052 5.00e-02 4.00e+02 7.80e-02 9.74e+00 pdb=" N PRO A 805 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 805 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 805 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 40 " -0.016 2.00e-02 2.50e+03 1.16e-02 3.37e+00 pdb=" CG TRP E 40 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP E 40 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP E 40 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 40 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 40 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 40 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 40 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 40 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 40 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 809 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO A 810 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 810 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 810 " -0.025 5.00e-02 4.00e+02 ... (remaining 2293 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 114 2.63 - 3.20: 12191 3.20 - 3.76: 19376 3.76 - 4.33: 25941 4.33 - 4.90: 42709 Nonbonded interactions: 100331 Sorted by model distance: nonbonded pdb=" OH TYR A 38 " pdb=" OE1 GLN A 153 " model vdw 2.059 3.040 nonbonded pdb=" OG1 THR B 787 " pdb=" OD1 ASP B 789 " model vdw 2.179 3.040 nonbonded pdb=" OG1 THR C 80 " pdb=" OE2 GLU A 366 " model vdw 2.199 3.040 nonbonded pdb=" O ASP A 342 " pdb=" ND1 HIS A 346 " model vdw 2.212 3.120 nonbonded pdb=" OH TYR B 495 " pdb=" OD1 ASP B 618 " model vdw 2.216 3.040 ... (remaining 100326 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 176 or (resid 177 a \ nd (name N or name CA or name C or name O or name CB )) or resid 178 through 237 \ or resid 241 through 431 or (resid 432 through 433 and (name N or name CA or na \ me C or name O or name CB )) or resid 441 through 498 or (resid 499 and (name N \ or name CA or name C or name O or name CB )) or resid 500 through 503 or resid 5 \ 15 through 531 or resid 607 through 622 or (resid 623 through 629 and (name N or \ name CA or name C or name O or name CB )) or resid 630 through 633 or (resid 63 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 635 through \ 638 or (resid 639 and (name N or name CA or name C or name O or name CB )) or re \ sid 640 or (resid 641 through 645 and (name N or name CA or name C or name O or \ name CB )) or (resid 646 through 648 and (name N or name CA or name C or name O \ or name CB )) or resid 649 through 662 or (resid 663 and (name N or name CA or n \ ame C or name O or name CB )) or resid 664 through 726 or (resid 727 and (name N \ or name CA or name C or name O or name CB )) or resid 728 or (resid 729 through \ 730 and (name N or name CA or name C or name O or name CB )) or resid 731 throu \ gh 740 or (resid 741 and (name N or name CA or name C or name O or name CB )) or \ resid 742 through 764 or (resid 765 through 776 and (name N or name CA or name \ C or name O or name CB )) or resid 777 through 821)) selection = (chain 'B' and (resid 15 through 53 or (resid 54 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 254 or (resid 255 throu \ gh 256 and (name N or name CA or name C or name O or name CB )) or resid 257 thr \ ough 296 or (resid 297 through 304 and (name N or name CA or name C or name O or \ name CB )) or resid 305 through 441 or (resid 442 and (name N or name CA or nam \ e C or name O or name CB )) or resid 443 through 493 or (resid 494 and (name N o \ r name CA or name C or name O or name CB )) or resid 495 through 606 or (resid 6 \ 07 through 608 and (name N or name CA or name C or name O or name CB )) or resid \ 609 through 657 or (resid 658 and (name N or name CA or name C or name O or nam \ e CB )) or resid 659 through 660 or (resid 661 through 663 and (name N or name C \ A or name C or name O or name CB )) or resid 664 through 690 or (resid 691 throu \ gh 697 and (name N or name CA or name C or name O or name CB )) or resid 698 thr \ ough 699 or (resid 700 and (name N or name CA or name C or name O or name CB )) \ or resid 701 through 703 or (resid 704 through 705 and (name N or name CA or nam \ e C or name O or name CB )) or resid 706 through 720 or (resid 721 and (name N o \ r name CA or name C or name O or name CB )) or resid 722 through 731 or (resid 7 \ 32 and (name N or name CA or name C or name O or name CB )) or resid 733 through \ 762 or (resid 763 and (name N or name CA or name C or name O or name CB )) or r \ esid 764 through 799 or (resid 800 and (name N or name CA or name C or name O or \ name CB )) or resid 801 through 818 or (resid 819 through 821 and (name N or na \ me CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'D' and (resid 13 through 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 36 or (resid 37 and (name N or nam \ e CA or name C or name O or name CB )) or resid 38 through 41 or (resid 42 throu \ gh 43 and (name N or name CA or name C or name O or name CB )) or resid 44 throu \ gh 45 or (resid 46 and (name N or name CA or name C or name O or name CB )) or r \ esid 47 through 62)) selection = (chain 'E' and ((resid 13 through 15 and (name N or name CA or name C or name O \ or name CB )) or resid 16 through 21 or (resid 22 and (name N or name CA or name \ C or name O or name CB )) or resid 23 through 54 or (resid 55 through 56 and (n \ ame N or name CA or name C or name O or name CB )) or resid 57 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: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.810 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 : 0.004 0.040 13042 Z= 0.214 Angle : 0.680 7.924 17722 Z= 0.397 Chirality : 0.042 0.326 1968 Planarity : 0.004 0.078 2296 Dihedral : 12.595 83.919 4521 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.20), residues: 1647 helix: 1.02 (0.19), residues: 735 sheet: -0.24 (0.33), residues: 268 loop : -1.39 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 40 HIS 0.006 0.001 HIS A 187 PHE 0.023 0.002 PHE D 61 TYR 0.018 0.002 TYR A 22 ARG 0.005 0.001 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.17393 ( 654) hydrogen bonds : angle 7.75542 ( 1932) covalent geometry : bond 0.00437 (13042) covalent geometry : angle 0.67965 (17722) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.481 Fit side-chains revert: symmetry clash REVERT: D 51 LEU cc_start: 0.8660 (mt) cc_final: 0.8427 (mt) REVERT: E 26 ARG cc_start: 0.7313 (mmm160) cc_final: 0.7012 (mmm160) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2300 time to fit residues: 50.4291 Evaluate side-chains 117 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 50.0000 chunk 126 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 130 optimal weight: 40.0000 chunk 50 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 151 optimal weight: 40.0000 overall best weight: 5.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.096046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.085815 restraints weight = 42055.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.087784 restraints weight = 21050.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.089056 restraints weight = 12858.826| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13042 Z= 0.167 Angle : 0.610 8.965 17722 Z= 0.325 Chirality : 0.042 0.242 1968 Planarity : 0.005 0.079 2296 Dihedral : 4.870 21.175 1806 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.06 % Allowed : 6.45 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1647 helix: 1.20 (0.19), residues: 749 sheet: -0.31 (0.33), residues: 264 loop : -1.39 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 40 HIS 0.006 0.001 HIS A 187 PHE 0.019 0.002 PHE B 478 TYR 0.016 0.002 TYR D 18 ARG 0.005 0.000 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 654) hydrogen bonds : angle 5.59129 ( 1932) covalent geometry : bond 0.00358 (13042) covalent geometry : angle 0.60963 (17722) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 1.405 Fit side-chains revert: symmetry clash REVERT: A 311 GLU cc_start: 0.7545 (tp30) cc_final: 0.7298 (tp30) REVERT: D 51 LEU cc_start: 0.8666 (mt) cc_final: 0.8429 (mt) outliers start: 13 outliers final: 8 residues processed: 140 average time/residue: 0.2069 time to fit residues: 45.2335 Evaluate side-chains 126 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain E residue 40 TRP Chi-restraints excluded: chain E residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 4 optimal weight: 30.0000 chunk 122 optimal weight: 20.0000 chunk 164 optimal weight: 8.9990 chunk 5 optimal weight: 0.3980 chunk 17 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 125 optimal weight: 30.0000 chunk 44 optimal weight: 5.9990 chunk 64 optimal weight: 30.0000 chunk 27 optimal weight: 8.9990 overall best weight: 6.8788 ------------------------------------------------------------------------------- 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 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN B 25 HIS ** B 153 GLN ** 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 = 0.3698 r_free = 0.3698 target = 0.095490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.085273 restraints weight = 42502.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.087233 restraints weight = 21298.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.088526 restraints weight = 13004.990| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13042 Z= 0.187 Angle : 0.596 8.661 17722 Z= 0.316 Chirality : 0.041 0.181 1968 Planarity : 0.005 0.079 2296 Dihedral : 4.813 19.863 1806 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.23 % Allowed : 10.62 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1647 helix: 1.23 (0.19), residues: 756 sheet: -0.44 (0.33), residues: 264 loop : -1.45 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 40 HIS 0.006 0.001 HIS A 187 PHE 0.030 0.002 PHE B 777 TYR 0.016 0.002 TYR D 17 ARG 0.005 0.000 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 654) hydrogen bonds : angle 5.34813 ( 1932) covalent geometry : bond 0.00403 (13042) covalent geometry : angle 0.59551 (17722) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 1.962 Fit side-chains revert: symmetry clash REVERT: C 28 MET cc_start: 0.8413 (ptp) cc_final: 0.8113 (ptm) REVERT: A 117 MET cc_start: 0.8250 (mtp) cc_final: 0.8042 (mtp) REVERT: A 311 GLU cc_start: 0.7685 (tp30) cc_final: 0.7396 (tp30) REVERT: A 633 MET cc_start: 0.6534 (mpp) cc_final: 0.6323 (mpp) REVERT: B 448 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7986 (mmm) REVERT: D 51 LEU cc_start: 0.8693 (mt) cc_final: 0.8481 (mt) outliers start: 15 outliers final: 11 residues processed: 132 average time/residue: 0.2477 time to fit residues: 52.4346 Evaluate side-chains 129 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 40 TRP Chi-restraints excluded: chain E residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 156 optimal weight: 30.0000 chunk 90 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 23 optimal weight: 50.0000 chunk 13 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 GLN ** 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 = 0.3686 r_free = 0.3686 target = 0.094735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.084550 restraints weight = 42444.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.086492 restraints weight = 21387.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.087750 restraints weight = 13105.163| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13042 Z= 0.198 Angle : 0.592 9.192 17722 Z= 0.314 Chirality : 0.041 0.156 1968 Planarity : 0.005 0.078 2296 Dihedral : 4.828 20.582 1806 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.21 % Allowed : 13.24 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.21), residues: 1647 helix: 1.22 (0.19), residues: 757 sheet: -0.53 (0.34), residues: 263 loop : -1.53 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 40 HIS 0.006 0.001 HIS A 187 PHE 0.019 0.002 PHE B 478 TYR 0.016 0.002 TYR B 251 ARG 0.003 0.000 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 654) hydrogen bonds : angle 5.25432 ( 1932) covalent geometry : bond 0.00430 (13042) covalent geometry : angle 0.59155 (17722) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: A 311 GLU cc_start: 0.7717 (tp30) cc_final: 0.7491 (tp30) REVERT: B 218 MET cc_start: 0.8359 (ppp) cc_final: 0.8079 (ppp) REVERT: B 635 TYR cc_start: 0.5200 (m-80) cc_final: 0.4399 (m-10) REVERT: B 759 MET cc_start: 0.7757 (ptm) cc_final: 0.7509 (ptm) REVERT: D 51 LEU cc_start: 0.8730 (mt) cc_final: 0.8512 (mt) outliers start: 27 outliers final: 23 residues processed: 138 average time/residue: 0.2294 time to fit residues: 51.2697 Evaluate side-chains 138 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 40 TRP Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 52 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 30.0000 chunk 88 optimal weight: 40.0000 chunk 16 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 121 optimal weight: 20.0000 chunk 135 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 HIS ** B 153 GLN ** 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 = 0.3693 r_free = 0.3693 target = 0.095678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.085293 restraints weight = 42457.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.087270 restraints weight = 21107.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.088578 restraints weight = 12847.231| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13042 Z= 0.122 Angle : 0.541 10.026 17722 Z= 0.282 Chirality : 0.040 0.144 1968 Planarity : 0.005 0.079 2296 Dihedral : 4.531 17.993 1806 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.80 % Allowed : 15.36 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1647 helix: 1.47 (0.19), residues: 758 sheet: -0.32 (0.34), residues: 251 loop : -1.46 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 40 HIS 0.005 0.001 HIS B 612 PHE 0.013 0.001 PHE B 478 TYR 0.017 0.001 TYR B 251 ARG 0.002 0.000 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 654) hydrogen bonds : angle 4.87734 ( 1932) covalent geometry : bond 0.00264 (13042) covalent geometry : angle 0.54064 (17722) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.371 Fit side-chains revert: symmetry clash REVERT: A 311 GLU cc_start: 0.7708 (tp30) cc_final: 0.7459 (tp30) REVERT: B 218 MET cc_start: 0.8337 (ppp) cc_final: 0.8043 (ppp) REVERT: B 635 TYR cc_start: 0.5041 (m-80) cc_final: 0.4342 (m-10) REVERT: D 49 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.7234 (t80) REVERT: D 51 LEU cc_start: 0.8720 (mt) cc_final: 0.8517 (mt) REVERT: E 17 TYR cc_start: 0.4569 (t80) cc_final: 0.4212 (t80) REVERT: E 49 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.6486 (m-80) outliers start: 22 outliers final: 16 residues processed: 138 average time/residue: 0.2013 time to fit residues: 44.4359 Evaluate side-chains 136 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain E residue 40 TRP Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 52 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 157 optimal weight: 40.0000 chunk 151 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 34 optimal weight: 20.0000 chunk 69 optimal weight: 0.8980 overall best weight: 2.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.096617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.086215 restraints weight = 42614.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.088223 restraints weight = 21041.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.089559 restraints weight = 12736.334| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13042 Z= 0.107 Angle : 0.522 10.069 17722 Z= 0.272 Chirality : 0.039 0.140 1968 Planarity : 0.004 0.078 2296 Dihedral : 4.307 15.378 1806 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.61 % Allowed : 15.20 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.21), residues: 1647 helix: 1.68 (0.19), residues: 754 sheet: -0.30 (0.34), residues: 250 loop : -1.45 (0.22), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 40 HIS 0.006 0.001 HIS B 612 PHE 0.016 0.001 PHE B 617 TYR 0.014 0.001 TYR B 251 ARG 0.002 0.000 ARG B 442 Details of bonding type rmsd hydrogen bonds : bond 0.03114 ( 654) hydrogen bonds : angle 4.64669 ( 1932) covalent geometry : bond 0.00230 (13042) covalent geometry : angle 0.52237 (17722) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 1.402 Fit side-chains revert: symmetry clash REVERT: A 245 MET cc_start: 0.8458 (mtp) cc_final: 0.8038 (ttt) REVERT: A 311 GLU cc_start: 0.7730 (tp30) cc_final: 0.7489 (tp30) REVERT: B 218 MET cc_start: 0.8321 (ppp) cc_final: 0.8044 (ppp) REVERT: B 448 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8171 (mmm) REVERT: B 612 HIS cc_start: 0.3031 (OUTLIER) cc_final: 0.2741 (p-80) REVERT: B 635 TYR cc_start: 0.5006 (m-80) cc_final: 0.4237 (m-10) REVERT: B 761 LEU cc_start: 0.5835 (mt) cc_final: 0.4792 (tt) REVERT: D 49 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.7282 (t80) REVERT: E 49 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.6464 (m-80) outliers start: 32 outliers final: 23 residues processed: 152 average time/residue: 0.2287 time to fit residues: 54.4336 Evaluate side-chains 144 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain E residue 40 TRP Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 52 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 73 optimal weight: 30.0000 chunk 44 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 64 optimal weight: 30.0000 chunk 165 optimal weight: 30.0000 chunk 41 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 17 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- 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 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 GLN ** 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 = 0.3698 r_free = 0.3698 target = 0.095321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.085210 restraints weight = 42257.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.087099 restraints weight = 21351.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.088344 restraints weight = 13165.562| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13042 Z= 0.201 Angle : 0.598 9.267 17722 Z= 0.315 Chirality : 0.041 0.162 1968 Planarity : 0.005 0.076 2296 Dihedral : 4.545 18.076 1806 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.78 % Allowed : 16.34 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.21), residues: 1647 helix: 1.47 (0.19), residues: 753 sheet: -0.35 (0.35), residues: 239 loop : -1.53 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 48 HIS 0.006 0.001 HIS A 187 PHE 0.047 0.002 PHE A 665 TYR 0.019 0.002 TYR A 38 ARG 0.003 0.000 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 654) hydrogen bonds : angle 4.98994 ( 1932) covalent geometry : bond 0.00439 (13042) covalent geometry : angle 0.59793 (17722) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 1.873 Fit side-chains revert: symmetry clash REVERT: A 245 MET cc_start: 0.8563 (mtp) cc_final: 0.7987 (ttt) REVERT: A 416 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8527 (tt) REVERT: B 218 MET cc_start: 0.8326 (ppp) cc_final: 0.8026 (ppp) REVERT: B 265 GLU cc_start: 0.7595 (pm20) cc_final: 0.7377 (pm20) REVERT: B 612 HIS cc_start: 0.3343 (OUTLIER) cc_final: 0.3034 (p-80) REVERT: B 635 TYR cc_start: 0.5271 (m-80) cc_final: 0.4408 (m-10) REVERT: B 759 MET cc_start: 0.7393 (ptm) cc_final: 0.7061 (ppp) REVERT: D 49 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.7295 (t80) outliers start: 34 outliers final: 27 residues processed: 143 average time/residue: 0.2074 time to fit residues: 47.5641 Evaluate side-chains 148 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 40 TRP Chi-restraints excluded: chain E residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 164 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 145 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 161 optimal weight: 30.0000 chunk 62 optimal weight: 7.9990 chunk 140 optimal weight: 20.0000 chunk 4 optimal weight: 30.0000 chunk 147 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 688 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.094584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.084472 restraints weight = 42561.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.086355 restraints weight = 21557.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.087601 restraints weight = 13313.689| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13042 Z= 0.213 Angle : 0.606 9.437 17722 Z= 0.321 Chirality : 0.042 0.171 1968 Planarity : 0.005 0.076 2296 Dihedral : 4.701 20.334 1806 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.51 % Allowed : 16.18 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.21), residues: 1647 helix: 1.33 (0.19), residues: 752 sheet: -0.59 (0.34), residues: 251 loop : -1.68 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 48 HIS 0.006 0.001 HIS A 187 PHE 0.023 0.002 PHE A 665 TYR 0.017 0.002 TYR A 38 ARG 0.004 0.000 ARG E 22 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 654) hydrogen bonds : angle 5.12974 ( 1932) covalent geometry : bond 0.00462 (13042) covalent geometry : angle 0.60582 (17722) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 1.487 Fit side-chains REVERT: A 245 MET cc_start: 0.8597 (mtp) cc_final: 0.8035 (ttt) REVERT: A 416 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8583 (tt) REVERT: B 218 MET cc_start: 0.8297 (ppp) cc_final: 0.7986 (ppp) REVERT: B 448 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8151 (mmm) REVERT: B 612 HIS cc_start: 0.3309 (OUTLIER) cc_final: 0.3015 (p-80) REVERT: B 635 TYR cc_start: 0.5428 (m-80) cc_final: 0.4539 (m-10) REVERT: B 789 ASP cc_start: 0.8309 (p0) cc_final: 0.8103 (p0) REVERT: D 49 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.7309 (t80) REVERT: E 32 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.7886 (t80) REVERT: E 49 PHE cc_start: 0.7072 (OUTLIER) cc_final: 0.6523 (m-80) outliers start: 43 outliers final: 28 residues processed: 155 average time/residue: 0.2123 time to fit residues: 52.0361 Evaluate side-chains 150 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 40 TRP Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 52 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 30 optimal weight: 7.9990 chunk 87 optimal weight: 20.0000 chunk 133 optimal weight: 10.0000 chunk 59 optimal weight: 0.4980 chunk 119 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 chunk 134 optimal weight: 20.0000 chunk 146 optimal weight: 30.0000 chunk 39 optimal weight: 20.0000 chunk 150 optimal weight: 30.0000 chunk 43 optimal weight: 2.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 688 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.096231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.085994 restraints weight = 42163.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.087947 restraints weight = 21202.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.089248 restraints weight = 12978.177| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13042 Z= 0.137 Angle : 0.578 9.955 17722 Z= 0.299 Chirality : 0.040 0.164 1968 Planarity : 0.005 0.077 2296 Dihedral : 4.493 18.707 1806 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.61 % Allowed : 17.73 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1647 helix: 1.48 (0.19), residues: 754 sheet: -0.52 (0.34), residues: 251 loop : -1.62 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 40 HIS 0.005 0.001 HIS B 612 PHE 0.032 0.001 PHE A 665 TYR 0.017 0.001 TYR D 17 ARG 0.002 0.000 ARG D 36 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 654) hydrogen bonds : angle 4.87226 ( 1932) covalent geometry : bond 0.00301 (13042) covalent geometry : angle 0.57751 (17722) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 1.468 Fit side-chains revert: symmetry clash REVERT: A 245 MET cc_start: 0.8544 (mtp) cc_final: 0.8055 (ttt) REVERT: B 218 MET cc_start: 0.8312 (ppp) cc_final: 0.7991 (ppp) REVERT: B 448 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8087 (mmm) REVERT: B 612 HIS cc_start: 0.3111 (OUTLIER) cc_final: 0.2815 (p-80) REVERT: B 635 TYR cc_start: 0.5414 (m-80) cc_final: 0.4516 (m-10) REVERT: B 761 LEU cc_start: 0.6014 (mt) cc_final: 0.5019 (mp) REVERT: D 49 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7294 (t80) REVERT: E 26 ARG cc_start: 0.7220 (mmm160) cc_final: 0.6960 (mmm160) REVERT: E 32 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7724 (t80) REVERT: E 49 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6657 (m-80) outliers start: 32 outliers final: 26 residues processed: 141 average time/residue: 0.2035 time to fit residues: 46.2722 Evaluate side-chains 149 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 40 TRP Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 86 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 53 optimal weight: 30.0000 chunk 36 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 688 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.095511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.085269 restraints weight = 42232.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.087192 restraints weight = 21292.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.088481 restraints weight = 13086.430| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13042 Z= 0.170 Angle : 0.585 9.757 17722 Z= 0.306 Chirality : 0.041 0.164 1968 Planarity : 0.005 0.077 2296 Dihedral : 4.539 19.186 1806 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.61 % Allowed : 17.48 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1647 helix: 1.45 (0.19), residues: 754 sheet: -0.53 (0.35), residues: 251 loop : -1.66 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 40 HIS 0.005 0.001 HIS B 612 PHE 0.029 0.002 PHE A 665 TYR 0.017 0.002 TYR E 17 ARG 0.003 0.000 ARG E 22 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 654) hydrogen bonds : angle 4.91580 ( 1932) covalent geometry : bond 0.00371 (13042) covalent geometry : angle 0.58477 (17722) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 1.398 Fit side-chains revert: symmetry clash REVERT: A 245 MET cc_start: 0.8578 (mtp) cc_final: 0.8052 (ttt) REVERT: B 218 MET cc_start: 0.8327 (ppp) cc_final: 0.8022 (ppp) REVERT: B 448 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8255 (mmm) REVERT: B 612 HIS cc_start: 0.3158 (OUTLIER) cc_final: 0.2860 (p-80) REVERT: B 635 TYR cc_start: 0.5437 (m-80) cc_final: 0.4478 (m-10) REVERT: B 761 LEU cc_start: 0.6015 (mt) cc_final: 0.4787 (mp) REVERT: D 49 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7316 (t80) REVERT: E 26 ARG cc_start: 0.7286 (mmm160) cc_final: 0.7018 (mmm160) REVERT: E 32 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7743 (t80) REVERT: E 49 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6533 (m-80) outliers start: 32 outliers final: 27 residues processed: 141 average time/residue: 0.2452 time to fit residues: 57.5719 Evaluate side-chains 147 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 40 TRP Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 117 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 35 optimal weight: 0.0970 chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 688 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.095981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.085761 restraints weight = 42161.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.087685 restraints weight = 21362.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.088948 restraints weight = 13170.959| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13042 Z= 0.151 Angle : 0.575 9.992 17722 Z= 0.300 Chirality : 0.040 0.164 1968 Planarity : 0.005 0.077 2296 Dihedral : 4.488 18.958 1806 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.78 % Allowed : 17.57 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1647 helix: 1.49 (0.19), residues: 752 sheet: -0.47 (0.35), residues: 250 loop : -1.66 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 40 HIS 0.005 0.001 HIS B 612 PHE 0.039 0.002 PHE A 214 TYR 0.016 0.001 TYR D 17 ARG 0.003 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03342 ( 654) hydrogen bonds : angle 4.83669 ( 1932) covalent geometry : bond 0.00330 (13042) covalent geometry : angle 0.57476 (17722) =============================================================================== Job complete usr+sys time: 3959.71 seconds wall clock time: 73 minutes 38.79 seconds (4418.79 seconds total)