Starting phenix.real_space_refine on Wed Mar 4 10:02:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oiu_12933/03_2026/7oiu_12933.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oiu_12933/03_2026/7oiu_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_12933/03_2026/7oiu_12933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oiu_12933/03_2026/7oiu_12933.map" model { file = "/net/cci-nas-00/data/ceres_data/7oiu_12933/03_2026/7oiu_12933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oiu_12933/03_2026/7oiu_12933.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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, 'HIS:plan': 1, 'TRP:plan': 2, 'ARG:plan': 2} 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: {'GLU:plan': 16, 'ASP:plan': 14, 'PHE:plan': 4, 'ARG:plan': 9, 'GLN:plan1': 7, 'HIS:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1} 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: {'ASP:plan': 9, 'GLN:plan1': 3, 'GLU:plan': 8, 'HIS:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 6} 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: {'GLU:plan': 3, 'GLN:plan1': 1, '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: {'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 3.17, per 1000 atoms: 0.25 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: 0.82 Conformation dependent library (CDL) restraints added in 504.0 milliseconds 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: 0.51 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: 2.40 Time building geometry restraints manager: 1.12 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: 0.190 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.740 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.800 ------------------------------------------------------------------------------- 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 : 10.36 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.001 ARG F 36 TYR 0.018 0.002 TYR A 22 PHE 0.023 0.002 PHE D 61 TRP 0.031 0.002 TRP E 40 HIS 0.006 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00437 (13042) covalent geometry : angle 0.67965 (17722) hydrogen bonds : bond 0.17393 ( 654) hydrogen bonds : angle 7.75542 ( 1932) *********************** 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 : 0.511 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: 0.1033 time to fit residues: 22.7373 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 : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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** A 390 ASN B 25 HIS B 97 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 790 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.095949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.085712 restraints weight = 42111.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.087675 restraints weight = 21158.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.088957 restraints weight = 12917.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.089790 restraints weight = 9011.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.090361 restraints weight = 6952.604| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13042 Z= 0.176 Angle : 0.614 8.798 17722 Z= 0.328 Chirality : 0.042 0.235 1968 Planarity : 0.005 0.079 2296 Dihedral : 4.897 21.479 1806 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.06 % Allowed : 6.62 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.20), residues: 1647 helix: 1.18 (0.19), residues: 744 sheet: -0.32 (0.33), residues: 264 loop : -1.40 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 36 TYR 0.016 0.002 TYR D 18 PHE 0.019 0.002 PHE B 478 TRP 0.015 0.001 TRP E 40 HIS 0.006 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00380 (13042) covalent geometry : angle 0.61376 (17722) hydrogen bonds : bond 0.04360 ( 654) hydrogen bonds : angle 5.67348 ( 1932) *********************** 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 151 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.476 Fit side-chains REVERT: A 311 GLU cc_start: 0.7484 (tp30) cc_final: 0.7251 (tp30) REVERT: D 51 LEU cc_start: 0.8632 (mt) cc_final: 0.8393 (mt) outliers start: 13 outliers final: 9 residues processed: 143 average time/residue: 0.0930 time to fit residues: 20.9261 Evaluate side-chains 127 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 199 LEU 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 91 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 chunk 162 optimal weight: 30.0000 chunk 34 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 89 optimal weight: 0.0030 chunk 109 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 overall best weight: 6.1998 ------------------------------------------------------------------------------- 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 B 25 HIS ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 612 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.095616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.085401 restraints weight = 42562.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.087372 restraints weight = 21381.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.088643 restraints weight = 13071.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.089485 restraints weight = 9141.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.090058 restraints weight = 7052.728| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1316 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= 0.173 Angle : 0.587 8.833 17722 Z= 0.311 Chirality : 0.041 0.179 1968 Planarity : 0.005 0.080 2296 Dihedral : 4.787 19.917 1806 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.06 % Allowed : 10.70 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.20), residues: 1647 helix: 1.24 (0.19), residues: 756 sheet: -0.42 (0.33), residues: 264 loop : -1.46 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 36 TYR 0.015 0.002 TYR D 17 PHE 0.029 0.002 PHE B 777 TRP 0.016 0.001 TRP E 40 HIS 0.006 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00376 (13042) covalent geometry : angle 0.58711 (17722) hydrogen bonds : bond 0.03993 ( 654) hydrogen bonds : angle 5.33430 ( 1932) *********************** 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 137 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: C 28 MET cc_start: 0.8291 (ptp) cc_final: 0.8087 (ptp) REVERT: A 117 MET cc_start: 0.8262 (mtp) cc_final: 0.8054 (mtp) REVERT: A 311 GLU cc_start: 0.7621 (tp30) cc_final: 0.7359 (tp30) REVERT: B 759 MET cc_start: 0.7678 (ptm) cc_final: 0.7212 (ppp) REVERT: D 51 LEU cc_start: 0.8656 (mt) cc_final: 0.8443 (mt) outliers start: 13 outliers final: 10 residues processed: 130 average time/residue: 0.0877 time to fit residues: 18.3235 Evaluate side-chains 128 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS 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 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 12 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 134 optimal weight: 0.0570 chunk 103 optimal weight: 9.9990 chunk 152 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 overall best weight: 5.4104 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.096113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.085843 restraints weight = 42512.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.087818 restraints weight = 21269.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.089091 restraints weight = 12987.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.089939 restraints weight = 9095.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.090517 restraints weight = 6996.221| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13042 Z= 0.155 Angle : 0.565 9.332 17722 Z= 0.297 Chirality : 0.040 0.150 1968 Planarity : 0.005 0.079 2296 Dihedral : 4.660 18.643 1806 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.88 % Allowed : 13.32 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.21), residues: 1647 helix: 1.37 (0.19), residues: 756 sheet: -0.44 (0.33), residues: 263 loop : -1.45 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 36 TYR 0.015 0.001 TYR B 251 PHE 0.014 0.001 PHE B 617 TRP 0.015 0.001 TRP E 40 HIS 0.006 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00336 (13042) covalent geometry : angle 0.56451 (17722) hydrogen bonds : bond 0.03602 ( 654) hydrogen bonds : angle 5.06200 ( 1932) *********************** 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 144 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.529 Fit side-chains REVERT: A 311 GLU cc_start: 0.7665 (tp30) cc_final: 0.7388 (tp30) REVERT: B 218 MET cc_start: 0.8314 (ppp) cc_final: 0.8088 (ppp) REVERT: B 635 TYR cc_start: 0.5165 (m-80) cc_final: 0.4354 (m-10) REVERT: D 49 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.7034 (t80) REVERT: D 51 LEU cc_start: 0.8639 (mt) cc_final: 0.8421 (mt) outliers start: 23 outliers final: 16 residues processed: 135 average time/residue: 0.0957 time to fit residues: 20.6627 Evaluate side-chains 129 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 486 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 125 VAL 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 D residue 49 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 24 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 111 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.094684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.084504 restraints weight = 42700.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.086406 restraints weight = 21575.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.087670 restraints weight = 13291.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.088496 restraints weight = 9328.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.088985 restraints weight = 7218.344| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13042 Z= 0.206 Angle : 0.599 9.375 17722 Z= 0.317 Chirality : 0.041 0.145 1968 Planarity : 0.005 0.077 2296 Dihedral : 4.784 20.390 1806 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.61 % Allowed : 14.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1647 helix: 1.28 (0.19), residues: 753 sheet: -0.57 (0.34), residues: 263 loop : -1.57 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 36 TYR 0.019 0.002 TYR B 251 PHE 0.017 0.002 PHE B 478 TRP 0.013 0.001 TRP E 40 HIS 0.007 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00449 (13042) covalent geometry : angle 0.59905 (17722) hydrogen bonds : bond 0.03826 ( 654) hydrogen bonds : angle 5.19539 ( 1932) *********************** 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 151 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.496 Fit side-chains REVERT: B 218 MET cc_start: 0.8296 (ppp) cc_final: 0.8033 (ppp) REVERT: B 635 TYR cc_start: 0.5153 (m-80) cc_final: 0.4397 (m-10) REVERT: D 49 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.7163 (t80) REVERT: D 51 LEU cc_start: 0.8710 (mt) cc_final: 0.8488 (mt) outliers start: 32 outliers final: 22 residues processed: 140 average time/residue: 0.0909 time to fit residues: 20.4692 Evaluate side-chains 139 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 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 273 THR Chi-restraints excluded: chain B residue 288 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 D residue 49 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 22 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 163 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 chunk 61 optimal weight: 40.0000 chunk 40 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.094503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.084329 restraints weight = 42538.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.086225 restraints weight = 21638.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.087483 restraints weight = 13369.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.088308 restraints weight = 9403.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.088869 restraints weight = 7283.537| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13042 Z= 0.205 Angle : 0.597 9.420 17722 Z= 0.316 Chirality : 0.041 0.143 1968 Planarity : 0.005 0.078 2296 Dihedral : 4.813 21.129 1806 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.02 % Allowed : 15.28 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.21), residues: 1647 helix: 1.26 (0.19), residues: 751 sheet: -0.67 (0.34), residues: 263 loop : -1.63 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 36 TYR 0.018 0.002 TYR B 251 PHE 0.032 0.002 PHE A 665 TRP 0.014 0.001 TRP C 48 HIS 0.006 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00444 (13042) covalent geometry : angle 0.59728 (17722) hydrogen bonds : bond 0.03780 ( 654) hydrogen bonds : angle 5.17020 ( 1932) *********************** 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 157 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 0.511 Fit side-chains REVERT: A 285 LYS cc_start: 0.7568 (mtmm) cc_final: 0.6784 (mtmm) REVERT: A 416 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8502 (tt) REVERT: B 218 MET cc_start: 0.8301 (ppp) cc_final: 0.7971 (ppp) REVERT: B 635 TYR cc_start: 0.5279 (m-80) cc_final: 0.4415 (m-10) REVERT: B 759 MET cc_start: 0.7681 (ptm) cc_final: 0.7370 (ppp) REVERT: B 789 ASP cc_start: 0.8223 (p0) cc_final: 0.8021 (p0) REVERT: D 49 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.7162 (t80) REVERT: D 51 LEU cc_start: 0.8714 (mt) cc_final: 0.8483 (mt) REVERT: E 49 PHE cc_start: 0.7070 (OUTLIER) cc_final: 0.6488 (m-80) outliers start: 37 outliers final: 32 residues processed: 147 average time/residue: 0.0903 time to fit residues: 21.4122 Evaluate side-chains 151 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 45 ASP 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 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 25 HIS 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 273 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 680 ASN 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 D residue 49 PHE 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 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 144 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 64 optimal weight: 30.0000 chunk 121 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 4 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.095593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.085444 restraints weight = 42123.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.087349 restraints weight = 21240.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.088612 restraints weight = 13057.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.089437 restraints weight = 9166.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.089935 restraints weight = 7101.402| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13042 Z= 0.151 Angle : 0.563 9.874 17722 Z= 0.296 Chirality : 0.040 0.156 1968 Planarity : 0.005 0.074 2296 Dihedral : 4.615 19.746 1806 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.02 % Allowed : 16.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.21), residues: 1647 helix: 1.41 (0.19), residues: 755 sheet: -0.48 (0.34), residues: 251 loop : -1.58 (0.22), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 36 TYR 0.016 0.001 TYR B 251 PHE 0.014 0.001 PHE B 617 TRP 0.014 0.001 TRP E 40 HIS 0.005 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00330 (13042) covalent geometry : angle 0.56318 (17722) hydrogen bonds : bond 0.03476 ( 654) hydrogen bonds : angle 4.94461 ( 1932) *********************** 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 157 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 0.482 Fit side-chains REVERT: B 218 MET cc_start: 0.8297 (ppp) cc_final: 0.7971 (ppp) REVERT: B 635 TYR cc_start: 0.5353 (m-80) cc_final: 0.4473 (m-10) REVERT: D 49 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.7246 (t80) REVERT: D 51 LEU cc_start: 0.8742 (mt) cc_final: 0.8516 (mt) REVERT: E 32 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7691 (t80) REVERT: E 49 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.6595 (m-80) outliers start: 37 outliers final: 28 residues processed: 146 average time/residue: 0.0904 time to fit residues: 21.2657 Evaluate side-chains 147 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 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 330 LEU 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 25 HIS 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 288 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 D residue 49 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 115 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 88 optimal weight: 40.0000 chunk 91 optimal weight: 20.0000 chunk 157 optimal weight: 40.0000 chunk 55 optimal weight: 20.0000 chunk 51 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 163 optimal weight: 40.0000 chunk 126 optimal weight: 8.9990 overall best weight: 5.6390 ------------------------------------------------------------------------------- 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 = 0.095438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.085292 restraints weight = 42166.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.087188 restraints weight = 21401.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.088446 restraints weight = 13194.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.089271 restraints weight = 9273.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.089841 restraints weight = 7178.654| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13042 Z= 0.160 Angle : 0.575 9.848 17722 Z= 0.301 Chirality : 0.040 0.161 1968 Planarity : 0.004 0.062 2296 Dihedral : 4.580 19.385 1806 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.51 % Allowed : 16.01 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.21), residues: 1647 helix: 1.42 (0.19), residues: 755 sheet: -0.52 (0.34), residues: 251 loop : -1.60 (0.22), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 36 TYR 0.016 0.001 TYR B 251 PHE 0.049 0.002 PHE A 665 TRP 0.014 0.001 TRP E 40 HIS 0.005 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00349 (13042) covalent geometry : angle 0.57548 (17722) hydrogen bonds : bond 0.03491 ( 654) hydrogen bonds : angle 4.96349 ( 1932) *********************** 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 164 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 0.487 Fit side-chains REVERT: A 416 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8475 (tt) REVERT: B 218 MET cc_start: 0.8284 (ppp) cc_final: 0.7959 (ppp) REVERT: B 635 TYR cc_start: 0.5366 (m-80) cc_final: 0.4486 (m-10) REVERT: D 49 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.7241 (t80) REVERT: D 51 LEU cc_start: 0.8729 (mt) cc_final: 0.8508 (mt) REVERT: E 26 ARG cc_start: 0.7272 (mmm160) cc_final: 0.6975 (mmm160) REVERT: E 32 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7719 (t80) REVERT: E 49 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6663 (m-80) outliers start: 43 outliers final: 33 residues processed: 155 average time/residue: 0.0884 time to fit residues: 22.1736 Evaluate side-chains 154 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 45 ASP 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 318 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 354 VAL 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 25 HIS 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 75 ASN 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 D residue 33 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 49 PHE 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 61 optimal weight: 30.0000 chunk 126 optimal weight: 3.9990 chunk 55 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 147 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 688 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.095831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.085413 restraints weight = 42513.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.087404 restraints weight = 21181.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.088714 restraints weight = 12876.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.089574 restraints weight = 8958.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.090152 restraints weight = 6862.715| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13042 Z= 0.114 Angle : 0.556 10.405 17722 Z= 0.286 Chirality : 0.039 0.152 1968 Planarity : 0.004 0.062 2296 Dihedral : 4.402 17.101 1806 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.45 % Allowed : 17.57 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.21), residues: 1647 helix: 1.61 (0.19), residues: 753 sheet: -0.42 (0.34), residues: 250 loop : -1.60 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 442 TYR 0.014 0.001 TYR A 709 PHE 0.029 0.001 PHE A 665 TRP 0.015 0.001 TRP E 40 HIS 0.004 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00247 (13042) covalent geometry : angle 0.55581 (17722) hydrogen bonds : bond 0.03183 ( 654) hydrogen bonds : angle 4.72564 ( 1932) *********************** 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 154 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.482 Fit side-chains REVERT: B 218 MET cc_start: 0.8309 (ppp) cc_final: 0.7976 (ppp) REVERT: B 448 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8175 (mmm) REVERT: B 635 TYR cc_start: 0.5448 (m-80) cc_final: 0.4457 (m-10) REVERT: B 761 LEU cc_start: 0.5687 (mt) cc_final: 0.4645 (mp) REVERT: D 49 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.7268 (t80) REVERT: D 51 LEU cc_start: 0.8690 (mt) cc_final: 0.8476 (mt) REVERT: E 26 ARG cc_start: 0.7236 (mmm160) cc_final: 0.6914 (mmm160) REVERT: E 32 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7645 (t80) REVERT: E 49 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6711 (m-80) outliers start: 30 outliers final: 22 residues processed: 147 average time/residue: 0.0888 time to fit residues: 20.9312 Evaluate side-chains 145 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 193 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 330 LEU 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 273 THR Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain E residue 32 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 89 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 32 optimal weight: 0.3980 chunk 116 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 135 optimal weight: 0.3980 chunk 41 optimal weight: 0.0970 chunk 81 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.5380 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.096764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.086341 restraints weight = 42587.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.088360 restraints weight = 21141.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.089666 restraints weight = 12817.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.090522 restraints weight = 8895.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.091118 restraints weight = 6829.402| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13042 Z= 0.106 Angle : 0.547 10.459 17722 Z= 0.282 Chirality : 0.039 0.164 1968 Planarity : 0.004 0.076 2296 Dihedral : 4.239 15.555 1806 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.21 % Allowed : 17.73 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.21), residues: 1647 helix: 1.77 (0.19), residues: 750 sheet: -0.34 (0.34), residues: 252 loop : -1.54 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 380 TYR 0.014 0.001 TYR A 709 PHE 0.036 0.001 PHE A 665 TRP 0.030 0.001 TRP A 377 HIS 0.004 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00233 (13042) covalent geometry : angle 0.54669 (17722) hydrogen bonds : bond 0.03027 ( 654) hydrogen bonds : angle 4.57295 ( 1932) ********************** 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 154 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.495 Fit side-chains REVERT: A 245 MET cc_start: 0.8558 (mtp) cc_final: 0.7864 (ttt) REVERT: A 377 TRP cc_start: 0.7615 (m100) cc_final: 0.7377 (m100) REVERT: A 416 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8389 (tt) REVERT: A 711 PHE cc_start: 0.7111 (t80) cc_final: 0.6840 (t80) REVERT: B 218 MET cc_start: 0.8291 (ppp) cc_final: 0.8001 (ppp) REVERT: B 448 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8138 (mmm) REVERT: B 635 TYR cc_start: 0.5388 (m-80) cc_final: 0.4346 (m-10) REVERT: B 761 LEU cc_start: 0.5466 (mt) cc_final: 0.4212 (mp) REVERT: D 49 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.7334 (t80) REVERT: E 26 ARG cc_start: 0.7271 (mmm160) cc_final: 0.6951 (mmm160) REVERT: E 32 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7584 (t80) REVERT: E 49 PHE cc_start: 0.7068 (OUTLIER) cc_final: 0.6729 (m-80) outliers start: 27 outliers final: 21 residues processed: 146 average time/residue: 0.0842 time to fit residues: 19.9357 Evaluate side-chains 148 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 193 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 318 SER 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 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 D residue 33 VAL Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain E residue 32 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 95 optimal weight: 20.0000 chunk 48 optimal weight: 0.3980 chunk 144 optimal weight: 30.0000 chunk 46 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 64 optimal weight: 30.0000 chunk 52 optimal weight: 9.9990 chunk 90 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 39 optimal weight: 9.9990 overall best weight: 6.6788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.095592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.085381 restraints weight = 42416.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.087290 restraints weight = 21588.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.088530 restraints weight = 13345.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.089378 restraints weight = 9425.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.089940 restraints weight = 7296.150| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13042 Z= 0.180 Angle : 0.588 9.837 17722 Z= 0.308 Chirality : 0.041 0.162 1968 Planarity : 0.005 0.060 2296 Dihedral : 4.467 17.156 1806 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.29 % Allowed : 17.89 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1647 helix: 1.55 (0.19), residues: 755 sheet: -0.48 (0.34), residues: 251 loop : -1.57 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 22 TYR 0.014 0.002 TYR B 251 PHE 0.026 0.002 PHE A 665 TRP 0.013 0.001 TRP C 48 HIS 0.006 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00393 (13042) covalent geometry : angle 0.58763 (17722) hydrogen bonds : bond 0.03395 ( 654) hydrogen bonds : angle 4.84325 ( 1932) =============================================================================== Job complete usr+sys time: 1902.43 seconds wall clock time: 33 minutes 46.59 seconds (2026.59 seconds total)