Starting phenix.real_space_refine on Mon May 19 12:34:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d84_46628/05_2025/9d84_46628.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d84_46628/05_2025/9d84_46628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d84_46628/05_2025/9d84_46628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d84_46628/05_2025/9d84_46628.map" model { file = "/net/cci-nas-00/data/ceres_data/9d84_46628/05_2025/9d84_46628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d84_46628/05_2025/9d84_46628.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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 90 5.16 5 C 11988 2.51 5 N 3264 2.21 5 O 3687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19029 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5828 Classifications: {'peptide': 774} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 743} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 515 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 64} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Restraints were copied for chains: D, F, C, E Time building chain proxies: 14.91, per 1000 atoms: 0.78 Number of scatterers: 19029 At special positions: 0 Unit cell: (101.004, 95.688, 195.806, 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 90 16.00 O 3687 8.00 N 3264 7.00 C 11988 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: 4.48 Conformation dependent library (CDL) restraints added in 2.4 seconds 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4500 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 39 sheets defined 26.5% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 10 through 13 Processing helix chain 'A' and resid 14 through 27 Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 157 through 165 Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.506A pdb=" N ILE A 173 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 209 removed outlier: 4.956A pdb=" N SER A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ALA A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 249 through 263 Proline residue: A 259 - end of helix Processing helix chain 'A' and resid 277 through 283 Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.900A pdb=" N GLN A 288 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.705A pdb=" N GLY A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 330 Processing helix chain 'A' and resid 348 through 365 removed outlier: 3.806A pdb=" N THR A 364 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR A 365 " --> pdb=" O MET A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 removed outlier: 3.556A pdb=" N GLU A 374 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 375 " --> pdb=" O ALA A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 371 through 375' Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 392 through 410 removed outlier: 3.567A pdb=" N GLY A 410 " --> pdb=" O MET A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.922A pdb=" N TRP A 501 " --> pdb=" O ASP A 497 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 497 through 502' Processing helix chain 'A' and resid 507 through 513 Processing helix chain 'A' and resid 535 through 539 removed outlier: 3.666A pdb=" N SER A 539 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 584 Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 635 through 640 Processing helix chain 'B' and resid 129 through 132 Processing helix chain 'C' and resid 10 through 13 Processing helix chain 'C' and resid 14 through 27 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 157 through 165 Processing helix chain 'C' and resid 168 through 173 removed outlier: 3.507A pdb=" N ILE C 173 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 209 removed outlier: 4.956A pdb=" N SER C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ALA C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 249 through 263 Proline residue: C 259 - end of helix Processing helix chain 'C' and resid 277 through 283 Processing helix chain 'C' and resid 284 through 288 removed outlier: 3.900A pdb=" N GLN C 288 " --> pdb=" O PRO C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.705A pdb=" N GLY C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 311 Processing helix chain 'C' and resid 312 through 330 Processing helix chain 'C' and resid 348 through 365 removed outlier: 3.806A pdb=" N THR C 364 " --> pdb=" O MET C 360 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR C 365 " --> pdb=" O MET C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 375 removed outlier: 3.556A pdb=" N GLU C 374 " --> pdb=" O ASN C 371 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C 375 " --> pdb=" O ALA C 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 371 through 375' Processing helix chain 'C' and resid 380 through 385 Processing helix chain 'C' and resid 392 through 410 removed outlier: 3.567A pdb=" N GLY C 410 " --> pdb=" O MET C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 502 removed outlier: 3.922A pdb=" N TRP C 501 " --> pdb=" O ASP C 497 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 497 through 502' Processing helix chain 'C' and resid 507 through 513 Processing helix chain 'C' and resid 535 through 539 removed outlier: 3.667A pdb=" N SER C 539 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 584 Processing helix chain 'C' and resid 628 through 632 Processing helix chain 'C' and resid 635 through 640 Processing helix chain 'D' and resid 129 through 132 Processing helix chain 'E' and resid 10 through 13 Processing helix chain 'E' and resid 14 through 27 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 87 through 94 Processing helix chain 'E' and resid 157 through 165 Processing helix chain 'E' and resid 168 through 173 removed outlier: 3.507A pdb=" N ILE E 173 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 209 removed outlier: 4.956A pdb=" N SER E 190 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ALA E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 226 Processing helix chain 'E' and resid 249 through 263 Proline residue: E 259 - end of helix Processing helix chain 'E' and resid 277 through 283 Processing helix chain 'E' and resid 284 through 288 removed outlier: 3.899A pdb=" N GLN E 288 " --> pdb=" O PRO E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.705A pdb=" N GLY E 306 " --> pdb=" O LEU E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 311 Processing helix chain 'E' and resid 312 through 330 Processing helix chain 'E' and resid 348 through 365 removed outlier: 3.806A pdb=" N THR E 364 " --> pdb=" O MET E 360 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR E 365 " --> pdb=" O MET E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 375 removed outlier: 3.556A pdb=" N GLU E 374 " --> pdb=" O ASN E 371 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL E 375 " --> pdb=" O ALA E 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 371 through 375' Processing helix chain 'E' and resid 380 through 385 Processing helix chain 'E' and resid 392 through 410 removed outlier: 3.567A pdb=" N GLY E 410 " --> pdb=" O MET E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 502 removed outlier: 3.922A pdb=" N TRP E 501 " --> pdb=" O ASP E 497 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP E 502 " --> pdb=" O ALA E 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 497 through 502' Processing helix chain 'E' and resid 507 through 513 Processing helix chain 'E' and resid 535 through 539 removed outlier: 3.666A pdb=" N SER E 539 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 584 Processing helix chain 'E' and resid 628 through 632 Processing helix chain 'E' and resid 635 through 640 Processing helix chain 'F' and resid 129 through 132 Processing sheet with id=1, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.487A pdb=" N VAL A 34 " --> pdb=" O TYR A 49 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 69 through 72 removed outlier: 7.118A pdb=" N VAL A 79 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU A 72 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL A 77 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 98 through 103 removed outlier: 6.208A pdb=" N VAL A 98 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N THR A 118 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ILE A 100 " --> pdb=" O THR A 118 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 265 through 272 Processing sheet with id=5, first strand: chain 'A' and resid 234 through 235 Processing sheet with id=6, first strand: chain 'A' and resid 423 through 425 Processing sheet with id=7, first strand: chain 'A' and resid 423 through 425 removed outlier: 5.349A pdb=" N LEU A 571 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N SER A 487 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 479 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA A 480 " --> pdb=" O ARG A 547 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG A 547 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 482 " --> pdb=" O VAL A 545 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 434 through 438 Processing sheet with id=9, first strand: chain 'A' and resid 597 through 605 removed outlier: 6.485A pdb=" N TYR A 663 " --> pdb=" O THR A 685 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR A 685 " --> pdb=" O TYR A 663 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU A 665 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE A 696 " --> pdb=" O GLY A 680 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 695 " --> pdb=" O THR A 750 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'A' and resid 597 through 605 removed outlier: 6.485A pdb=" N TYR A 663 " --> pdb=" O THR A 685 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR A 685 " --> pdb=" O TYR A 663 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU A 665 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE A 696 " --> pdb=" O GLY A 680 " (cutoff:3.500A) removed outlier: 13.482A pdb=" N ALA A 698 " --> pdb=" O THR A 733 " (cutoff:3.500A) removed outlier: 10.500A pdb=" N THR A 733 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N ALA A 700 " --> pdb=" O TYR A 731 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N TYR A 731 " --> pdb=" O ALA A 700 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N HIS A 702 " --> pdb=" O ALA A 729 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ALA A 729 " --> pdb=" O HIS A 702 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A 704 " --> pdb=" O ASP A 727 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 723 " --> pdb=" O LEU A 708 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'A' and resid 618 through 619 Processing sheet with id=12, first strand: chain 'B' and resid 124 through 127 removed outlier: 4.287A pdb=" N GLU B 151 " --> pdb=" O MET B 189 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'B' and resid 134 through 141 removed outlier: 6.362A pdb=" N ALA B 134 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N LEU B 180 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLY B 136 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N GLN B 178 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR B 138 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 173 " --> pdb=" O ASN B 168 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 33 through 35 removed outlier: 6.487A pdb=" N VAL C 34 " --> pdb=" O TYR C 49 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 69 through 72 removed outlier: 7.118A pdb=" N VAL C 79 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU C 72 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL C 77 " --> pdb=" O LEU C 72 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 98 through 103 removed outlier: 6.207A pdb=" N VAL C 98 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N THR C 118 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ILE C 100 " --> pdb=" O THR C 118 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'C' and resid 265 through 272 Processing sheet with id=18, first strand: chain 'C' and resid 234 through 235 Processing sheet with id=19, first strand: chain 'C' and resid 423 through 425 Processing sheet with id=20, first strand: chain 'C' and resid 423 through 425 removed outlier: 5.349A pdb=" N LEU C 571 " --> pdb=" O SER C 487 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N SER C 487 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 479 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA C 480 " --> pdb=" O ARG C 547 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG C 547 " --> pdb=" O ALA C 480 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE C 482 " --> pdb=" O VAL C 545 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'C' and resid 434 through 438 Processing sheet with id=22, first strand: chain 'C' and resid 597 through 605 removed outlier: 6.485A pdb=" N TYR C 663 " --> pdb=" O THR C 685 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR C 685 " --> pdb=" O TYR C 663 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU C 665 " --> pdb=" O LEU C 683 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE C 696 " --> pdb=" O GLY C 680 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C 695 " --> pdb=" O THR C 750 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'C' and resid 597 through 605 removed outlier: 6.485A pdb=" N TYR C 663 " --> pdb=" O THR C 685 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR C 685 " --> pdb=" O TYR C 663 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU C 665 " --> pdb=" O LEU C 683 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE C 696 " --> pdb=" O GLY C 680 " (cutoff:3.500A) removed outlier: 13.482A pdb=" N ALA C 698 " --> pdb=" O THR C 733 " (cutoff:3.500A) removed outlier: 10.499A pdb=" N THR C 733 " --> pdb=" O ALA C 698 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N ALA C 700 " --> pdb=" O TYR C 731 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N TYR C 731 " --> pdb=" O ALA C 700 " (cutoff:3.500A) removed outlier: 10.520A pdb=" N HIS C 702 " --> pdb=" O ALA C 729 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ALA C 729 " --> pdb=" O HIS C 702 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER C 704 " --> pdb=" O ASP C 727 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE C 723 " --> pdb=" O LEU C 708 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'C' and resid 618 through 619 Processing sheet with id=25, first strand: chain 'D' and resid 124 through 127 removed outlier: 4.288A pdb=" N GLU D 151 " --> pdb=" O MET D 189 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'D' and resid 134 through 141 removed outlier: 6.362A pdb=" N ALA D 134 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N LEU D 180 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLY D 136 " --> pdb=" O GLN D 178 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N GLN D 178 " --> pdb=" O GLY D 136 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR D 138 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR D 173 " --> pdb=" O ASN D 168 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'E' and resid 33 through 35 removed outlier: 6.486A pdb=" N VAL E 34 " --> pdb=" O TYR E 49 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'E' and resid 69 through 72 removed outlier: 7.118A pdb=" N VAL E 79 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU E 72 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL E 77 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'E' and resid 98 through 103 removed outlier: 6.208A pdb=" N VAL E 98 " --> pdb=" O ILE E 116 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR E 118 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N ILE E 100 " --> pdb=" O THR E 118 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'E' and resid 265 through 272 Processing sheet with id=31, first strand: chain 'E' and resid 234 through 235 Processing sheet with id=32, first strand: chain 'E' and resid 423 through 425 Processing sheet with id=33, first strand: chain 'E' and resid 423 through 425 removed outlier: 5.349A pdb=" N LEU E 571 " --> pdb=" O SER E 487 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N SER E 487 " --> pdb=" O LEU E 571 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA E 479 " --> pdb=" O VAL E 579 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA E 480 " --> pdb=" O ARG E 547 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG E 547 " --> pdb=" O ALA E 480 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE E 482 " --> pdb=" O VAL E 545 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'E' and resid 434 through 438 Processing sheet with id=35, first strand: chain 'E' and resid 597 through 605 removed outlier: 6.484A pdb=" N TYR E 663 " --> pdb=" O THR E 685 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR E 685 " --> pdb=" O TYR E 663 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU E 665 " --> pdb=" O LEU E 683 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE E 696 " --> pdb=" O GLY E 680 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA E 695 " --> pdb=" O THR E 750 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'E' and resid 597 through 605 removed outlier: 6.484A pdb=" N TYR E 663 " --> pdb=" O THR E 685 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR E 685 " --> pdb=" O TYR E 663 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU E 665 " --> pdb=" O LEU E 683 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE E 696 " --> pdb=" O GLY E 680 " (cutoff:3.500A) removed outlier: 13.482A pdb=" N ALA E 698 " --> pdb=" O THR E 733 " (cutoff:3.500A) removed outlier: 10.499A pdb=" N THR E 733 " --> pdb=" O ALA E 698 " (cutoff:3.500A) removed outlier: 9.711A pdb=" N ALA E 700 " --> pdb=" O TYR E 731 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N TYR E 731 " --> pdb=" O ALA E 700 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N HIS E 702 " --> pdb=" O ALA E 729 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ALA E 729 " --> pdb=" O HIS E 702 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER E 704 " --> pdb=" O ASP E 727 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE E 723 " --> pdb=" O LEU E 708 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'E' and resid 618 through 619 Processing sheet with id=38, first strand: chain 'F' and resid 124 through 127 removed outlier: 4.288A pdb=" N GLU F 151 " --> pdb=" O MET F 189 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'F' and resid 134 through 141 removed outlier: 6.362A pdb=" N ALA F 134 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N LEU F 180 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLY F 136 " --> pdb=" O GLN F 178 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N GLN F 178 " --> pdb=" O GLY F 136 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR F 138 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR F 173 " --> pdb=" O ASN F 168 " (cutoff:3.500A) 843 hydrogen bonds defined for protein. 2196 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: 7.93 Time building geometry restraints manager: 5.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3174 1.30 - 1.43: 5199 1.43 - 1.55: 10932 1.55 - 1.68: 0 1.68 - 1.81: 159 Bond restraints: 19464 Sorted by residual: bond pdb=" CA ALA C 775 " pdb=" CB ALA C 775 " ideal model delta sigma weight residual 1.528 1.437 0.091 1.58e-02 4.01e+03 3.31e+01 bond pdb=" CA ALA A 775 " pdb=" CB ALA A 775 " ideal model delta sigma weight residual 1.528 1.437 0.091 1.58e-02 4.01e+03 3.30e+01 bond pdb=" CA ALA E 775 " pdb=" CB ALA E 775 " ideal model delta sigma weight residual 1.528 1.437 0.091 1.58e-02 4.01e+03 3.29e+01 bond pdb=" CA SER A 776 " pdb=" CB SER A 776 " ideal model delta sigma weight residual 1.532 1.433 0.099 1.82e-02 3.02e+03 2.96e+01 bond pdb=" CA SER E 776 " pdb=" CB SER E 776 " ideal model delta sigma weight residual 1.532 1.433 0.099 1.82e-02 3.02e+03 2.96e+01 ... (remaining 19459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 24840 1.31 - 2.63: 1263 2.63 - 3.94: 279 3.94 - 5.25: 108 5.25 - 6.56: 24 Bond angle restraints: 26514 Sorted by residual: angle pdb=" N ILE B 147 " pdb=" CA ILE B 147 " pdb=" C ILE B 147 " ideal model delta sigma weight residual 112.83 107.21 5.62 9.90e-01 1.02e+00 3.22e+01 angle pdb=" N ILE F 147 " pdb=" CA ILE F 147 " pdb=" C ILE F 147 " ideal model delta sigma weight residual 112.83 107.21 5.62 9.90e-01 1.02e+00 3.22e+01 angle pdb=" N ILE D 147 " pdb=" CA ILE D 147 " pdb=" C ILE D 147 " ideal model delta sigma weight residual 112.83 107.22 5.61 9.90e-01 1.02e+00 3.21e+01 angle pdb=" N TYR C 509 " pdb=" CA TYR C 509 " pdb=" C TYR C 509 " ideal model delta sigma weight residual 113.28 107.68 5.60 1.22e+00 6.72e-01 2.11e+01 angle pdb=" N TYR E 509 " pdb=" CA TYR E 509 " pdb=" C TYR E 509 " ideal model delta sigma weight residual 113.28 107.69 5.59 1.22e+00 6.72e-01 2.10e+01 ... (remaining 26509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 10032 16.76 - 33.53: 954 33.53 - 50.29: 222 50.29 - 67.05: 63 67.05 - 83.82: 15 Dihedral angle restraints: 11286 sinusoidal: 4152 harmonic: 7134 Sorted by residual: dihedral pdb=" CA GLY C 129 " pdb=" C GLY C 129 " pdb=" N ALA C 130 " pdb=" CA ALA C 130 " ideal model delta harmonic sigma weight residual -180.00 -135.86 -44.14 0 5.00e+00 4.00e-02 7.79e+01 dihedral pdb=" CA GLY E 129 " pdb=" C GLY E 129 " pdb=" N ALA E 130 " pdb=" CA ALA E 130 " ideal model delta harmonic sigma weight residual -180.00 -135.86 -44.14 0 5.00e+00 4.00e-02 7.79e+01 dihedral pdb=" CA GLY A 129 " pdb=" C GLY A 129 " pdb=" N ALA A 130 " pdb=" CA ALA A 130 " ideal model delta harmonic sigma weight residual 180.00 -135.87 -44.13 0 5.00e+00 4.00e-02 7.79e+01 ... (remaining 11283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2077 0.042 - 0.083: 606 0.083 - 0.125: 238 0.125 - 0.167: 16 0.167 - 0.208: 15 Chirality restraints: 2952 Sorted by residual: chirality pdb=" CA PRO B 143 " pdb=" N PRO B 143 " pdb=" C PRO B 143 " pdb=" CB PRO B 143 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA PRO F 143 " pdb=" N PRO F 143 " pdb=" C PRO F 143 " pdb=" CB PRO F 143 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA PRO D 143 " pdb=" N PRO D 143 " pdb=" C PRO D 143 " pdb=" CB PRO D 143 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2949 not shown) Planarity restraints: 3456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN F 171 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.45e+00 pdb=" C ASN F 171 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN F 171 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU F 172 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 171 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.45e+00 pdb=" C ASN B 171 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN B 171 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU B 172 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 171 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C ASN D 171 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN D 171 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU D 172 " -0.014 2.00e-02 2.50e+03 ... (remaining 3453 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 244 2.52 - 3.11: 14695 3.11 - 3.71: 33015 3.71 - 4.30: 49485 4.30 - 4.90: 79877 Nonbonded interactions: 177316 Sorted by model distance: nonbonded pdb=" OH TYR A 609 " pdb=" OD1 ASN E 529 " model vdw 1.924 3.040 nonbonded pdb=" OD1 ASN C 529 " pdb=" OH TYR E 609 " model vdw 1.925 3.040 nonbonded pdb=" OD1 ASN A 529 " pdb=" OH TYR C 609 " model vdw 1.925 3.040 nonbonded pdb=" NH2 ARG C 598 " pdb=" OE1 GLU E 763 " model vdw 2.005 3.120 nonbonded pdb=" OE1 GLU A 763 " pdb=" NH2 ARG E 598 " model vdw 2.006 3.120 ... (remaining 177311 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: 0.14 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } 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 individual isotropic 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: 12.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 47.520 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4448 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 : 0.005 0.099 19464 Z= 0.271 Angle : 0.734 6.565 26514 Z= 0.459 Chirality : 0.046 0.208 2952 Planarity : 0.004 0.043 3456 Dihedral : 14.821 83.815 6786 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.10 % Favored : 96.78 % Rotamer: Outliers : 1.25 % Allowed : 15.32 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.17), residues: 2517 helix: 1.02 (0.23), residues: 531 sheet: -0.13 (0.20), residues: 624 loop : -0.10 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 203 HIS 0.006 0.002 HIS E 481 PHE 0.018 0.001 PHE E 5 TYR 0.018 0.002 TYR E 250 ARG 0.004 0.001 ARG E 24 Details of bonding type rmsd hydrogen bonds : bond 0.20585 ( 741) hydrogen bonds : angle 8.93646 ( 2196) covalent geometry : bond 0.00468 (19464) covalent geometry : angle 0.73386 (26514) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 439 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.7924 (mp10) cc_final: 0.7570 (mp10) REVERT: A 144 SER cc_start: 0.7750 (OUTLIER) cc_final: 0.7517 (p) REVERT: A 224 THR cc_start: 0.7700 (m) cc_final: 0.7444 (m) REVERT: A 250 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7654 (p90) REVERT: A 304 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8217 (m-30) REVERT: A 385 GLN cc_start: 0.6933 (mm-40) cc_final: 0.6719 (mm-40) REVERT: A 609 TYR cc_start: 0.7248 (t80) cc_final: 0.7045 (t80) REVERT: C 144 SER cc_start: 0.4669 (OUTLIER) cc_final: 0.4122 (p) REVERT: D 189 MET cc_start: 0.2908 (mmt) cc_final: 0.2105 (tpp) REVERT: E 34 VAL cc_start: 0.6306 (p) cc_final: 0.6094 (p) REVERT: E 364 THR cc_start: 0.5385 (m) cc_final: 0.4294 (t) REVERT: F 152 ILE cc_start: 0.3659 (mm) cc_final: 0.3171 (mm) outliers start: 25 outliers final: 4 residues processed: 459 average time/residue: 1.0019 time to fit residues: 533.4047 Evaluate side-chains 275 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 267 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain F residue 144 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 0.0020 chunk 188 optimal weight: 1.9990 chunk 104 optimal weight: 0.0570 chunk 64 optimal weight: 2.9990 chunk 127 optimal weight: 0.0370 chunk 100 optimal weight: 0.6980 chunk 195 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 145 optimal weight: 0.0980 chunk 226 optimal weight: 0.3980 overall best weight: 0.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 GLN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN A 337 GLN A 515 ASN ** A 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS A 610 ASN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 209 HIS C 261 GLN C 276 HIS C 280 GLN C 337 GLN C 352 ASN C 399 HIS ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 HIS D 130 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN ** E 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 ASN ** E 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 HIS E 622 ASN E 761 ASN F 178 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.140870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.127264 restraints weight = 33352.273| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.74 r_work: 0.3673 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5202 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19464 Z= 0.149 Angle : 0.659 15.164 26514 Z= 0.347 Chirality : 0.045 0.195 2952 Planarity : 0.005 0.045 3456 Dihedral : 5.259 50.130 2739 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.75 % Allowed : 19.02 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2517 helix: 0.71 (0.23), residues: 534 sheet: -0.29 (0.20), residues: 612 loop : -0.18 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 590 HIS 0.007 0.001 HIS E 651 PHE 0.019 0.002 PHE C 36 TYR 0.018 0.002 TYR E 538 ARG 0.008 0.001 ARG E 598 Details of bonding type rmsd hydrogen bonds : bond 0.04491 ( 741) hydrogen bonds : angle 6.39477 ( 2196) covalent geometry : bond 0.00336 (19464) covalent geometry : angle 0.65922 (26514) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 329 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.7872 (mp10) cc_final: 0.7494 (mp10) REVERT: A 144 SER cc_start: 0.8135 (m) cc_final: 0.7863 (p) REVERT: A 224 THR cc_start: 0.7552 (m) cc_final: 0.7338 (m) REVERT: A 250 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7558 (p90) REVERT: A 385 GLN cc_start: 0.6616 (mm-40) cc_final: 0.6315 (mm-40) REVERT: A 754 THR cc_start: 0.8184 (p) cc_final: 0.7928 (t) REVERT: B 185 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6792 (tm-30) REVERT: C 132 PRO cc_start: 0.6655 (Cg_endo) cc_final: 0.6369 (Cg_exo) REVERT: C 296 VAL cc_start: 0.4573 (OUTLIER) cc_final: 0.4192 (p) REVERT: C 365 TYR cc_start: 0.4884 (m-80) cc_final: 0.4638 (m-80) REVERT: F 152 ILE cc_start: 0.5268 (mm) cc_final: 0.4484 (mm) outliers start: 95 outliers final: 17 residues processed: 387 average time/residue: 0.9336 time to fit residues: 424.7124 Evaluate side-chains 273 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 253 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 705 MET Chi-restraints excluded: chain E residue 763 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 128 optimal weight: 1.9990 chunk 170 optimal weight: 0.1980 chunk 210 optimal weight: 0.0670 chunk 45 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 214 optimal weight: 0.4980 chunk 69 optimal weight: 0.1980 chunk 141 optimal weight: 0.4980 chunk 195 optimal weight: 0.4980 chunk 192 optimal weight: 1.9990 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 ASN A 611 GLN B 171 ASN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN C 239 ASN ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN D 168 ASN E 25 HIS ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN E 390 HIS ** E 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN E 622 ASN E 702 HIS F 160 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.134823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.118907 restraints weight = 32719.181| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.82 r_work: 0.3586 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 19464 Z= 0.212 Angle : 0.753 14.450 26514 Z= 0.397 Chirality : 0.049 0.259 2952 Planarity : 0.005 0.057 3456 Dihedral : 5.245 53.271 2728 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.50 % Allowed : 20.42 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 2517 helix: 0.51 (0.23), residues: 483 sheet: -0.53 (0.20), residues: 648 loop : -0.21 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 354 HIS 0.010 0.002 HIS C 390 PHE 0.037 0.003 PHE C 558 TYR 0.019 0.002 TYR A 663 ARG 0.012 0.001 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.04534 ( 741) hydrogen bonds : angle 6.22286 ( 2196) covalent geometry : bond 0.00474 (19464) covalent geometry : angle 0.75338 (26514) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 376 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 SER cc_start: 0.8477 (m) cc_final: 0.8231 (p) REVERT: A 314 ASP cc_start: 0.8544 (m-30) cc_final: 0.8218 (m-30) REVERT: A 385 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7382 (mm-40) REVERT: A 769 MET cc_start: 0.8571 (mpp) cc_final: 0.8222 (mtt) REVERT: B 189 MET cc_start: 0.7873 (mmm) cc_final: 0.7490 (mmt) REVERT: C 17 THR cc_start: 0.6179 (OUTLIER) cc_final: 0.5976 (t) REVERT: C 338 THR cc_start: 0.6334 (m) cc_final: 0.6114 (p) REVERT: C 522 ASN cc_start: 0.7250 (OUTLIER) cc_final: 0.6994 (m-40) REVERT: C 692 GLN cc_start: 0.6114 (OUTLIER) cc_final: 0.5813 (mm110) REVERT: C 751 TRP cc_start: 0.3727 (OUTLIER) cc_final: 0.3148 (m-10) REVERT: D 129 ASN cc_start: 0.7930 (t0) cc_final: 0.7527 (t0) REVERT: E 163 GLU cc_start: 0.6446 (tm-30) cc_final: 0.5628 (pt0) REVERT: E 206 LYS cc_start: 0.6039 (OUTLIER) cc_final: 0.5837 (ttpp) REVERT: E 248 MET cc_start: 0.3324 (OUTLIER) cc_final: 0.3095 (tmm) REVERT: E 452 TYR cc_start: 0.6151 (m-80) cc_final: 0.5743 (m-80) REVERT: E 478 GLU cc_start: 0.6144 (OUTLIER) cc_final: 0.5525 (mt-10) REVERT: E 554 LYS cc_start: 0.6178 (OUTLIER) cc_final: 0.5845 (ptpt) REVERT: F 152 ILE cc_start: 0.5631 (mm) cc_final: 0.4888 (mm) outliers start: 90 outliers final: 27 residues processed: 433 average time/residue: 0.8710 time to fit residues: 447.1337 Evaluate side-chains 331 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 296 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 522 ASN Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 646 PHE Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 747 ILE Chi-restraints excluded: chain C residue 751 TRP Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 377 TYR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 478 GLU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 710 VAL Chi-restraints excluded: chain E residue 747 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 176 optimal weight: 1.9990 chunk 196 optimal weight: 0.3980 chunk 130 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 194 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 228 optimal weight: 0.0870 chunk 94 optimal weight: 3.9990 overall best weight: 0.4960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 119 HIS A 209 HIS ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 GLN A 607 GLN B 178 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN C 276 HIS C 421 ASN ** C 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 ASN C 577 GLN C 597 HIS E 25 HIS ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 ASN E 381 ASN E 385 GLN ** E 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 GLN E 424 ASN E 528 ASN E 572 ASN E 611 GLN E 651 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.119896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.099850 restraints weight = 31549.356| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.81 r_work: 0.3293 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 1.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.141 19464 Z= 0.307 Angle : 0.899 18.511 26514 Z= 0.472 Chirality : 0.054 0.425 2952 Planarity : 0.007 0.140 3456 Dihedral : 5.902 47.648 2726 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 6.51 % Allowed : 20.52 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2517 helix: -0.35 (0.22), residues: 519 sheet: -0.74 (0.20), residues: 642 loop : -0.35 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP C 354 HIS 0.019 0.003 HIS E 276 PHE 0.028 0.003 PHE E 471 TYR 0.029 0.003 TYR C 452 ARG 0.014 0.001 ARG E 357 Details of bonding type rmsd hydrogen bonds : bond 0.05177 ( 741) hydrogen bonds : angle 6.59640 ( 2196) covalent geometry : bond 0.00659 (19464) covalent geometry : angle 0.89945 (26514) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 361 time to evaluate : 2.116 Fit side-chains revert: symmetry clash REVERT: A 111 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8421 (mp-120) REVERT: A 144 SER cc_start: 0.8691 (m) cc_final: 0.8360 (p) REVERT: A 314 ASP cc_start: 0.8980 (m-30) cc_final: 0.8610 (m-30) REVERT: A 358 MET cc_start: 0.9123 (pp-130) cc_final: 0.8851 (tmm) REVERT: A 753 SER cc_start: 0.9165 (OUTLIER) cc_final: 0.8864 (t) REVERT: C 250 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.5258 (t80) REVERT: C 669 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8117 (tp) REVERT: C 705 MET cc_start: 0.8393 (mmm) cc_final: 0.8152 (mmm) REVERT: D 181 GLU cc_start: 0.7495 (tt0) cc_final: 0.7283 (tt0) REVERT: E 24 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8076 (tpp-160) REVERT: E 248 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7279 (tmm) REVERT: E 276 HIS cc_start: 0.5510 (OUTLIER) cc_final: 0.5245 (t-90) REVERT: E 294 ASP cc_start: 0.6102 (OUTLIER) cc_final: 0.5703 (t0) REVERT: E 304 ASP cc_start: 0.7832 (m-30) cc_final: 0.7559 (m-30) REVERT: E 730 SER cc_start: 0.8086 (OUTLIER) cc_final: 0.7865 (p) REVERT: E 747 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7780 (mt) REVERT: F 129 ASN cc_start: 0.7926 (t0) cc_final: 0.7661 (t0) REVERT: F 152 ILE cc_start: 0.7282 (mm) cc_final: 0.6497 (mm) REVERT: F 155 GLU cc_start: 0.7297 (tp30) cc_final: 0.6857 (tp30) outliers start: 130 outliers final: 24 residues processed: 441 average time/residue: 1.0022 time to fit residues: 513.0493 Evaluate side-chains 277 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 646 PHE Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 276 HIS Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 377 TYR Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 669 ILE Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 730 SER Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain F residue 154 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 138 optimal weight: 0.6980 chunk 170 optimal weight: 0.3980 chunk 136 optimal weight: 0.6980 chunk 242 optimal weight: 0.9990 chunk 222 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 160 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 217 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN A 209 HIS ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN A 529 ASN A 691 ASN B 160 GLN C 30 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN C 276 HIS C 352 ASN C 371 ASN C 421 ASN C 485 HIS C 519 ASN C 522 ASN C 529 ASN D 159 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 ASN E 245 HIS ** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 390 HIS ** E 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 GLN E 424 ASN E 529 ASN F 160 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.081490 restraints weight = 31758.048| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.75 r_work: 0.2990 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 1.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19464 Z= 0.223 Angle : 0.705 14.362 26514 Z= 0.364 Chirality : 0.048 0.250 2952 Planarity : 0.005 0.063 3456 Dihedral : 5.359 47.470 2726 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.70 % Allowed : 23.22 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2517 helix: 0.27 (0.23), residues: 495 sheet: -0.63 (0.20), residues: 633 loop : -0.22 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 152 HIS 0.007 0.001 HIS E 276 PHE 0.019 0.002 PHE C 559 TYR 0.024 0.002 TYR E 377 ARG 0.013 0.001 ARG E 417 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 741) hydrogen bonds : angle 6.05802 ( 2196) covalent geometry : bond 0.00512 (19464) covalent geometry : angle 0.70454 (26514) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 266 time to evaluate : 1.918 Fit side-chains REVERT: A 314 ASP cc_start: 0.8998 (m-30) cc_final: 0.8622 (m-30) REVERT: A 358 MET cc_start: 0.9233 (pp-130) cc_final: 0.8993 (tmm) REVERT: A 753 SER cc_start: 0.9136 (OUTLIER) cc_final: 0.8873 (t) REVERT: C 46 LYS cc_start: 0.7492 (ptpt) cc_final: 0.7277 (ptpt) REVERT: C 179 LYS cc_start: 0.7705 (ptmt) cc_final: 0.7327 (ptmm) REVERT: C 248 MET cc_start: 0.9045 (tpp) cc_final: 0.8632 (tpp) REVERT: C 317 MET cc_start: 0.7917 (tpt) cc_final: 0.7645 (tpt) REVERT: C 326 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.6838 (ttp80) REVERT: C 583 MET cc_start: 0.9070 (ttt) cc_final: 0.8827 (tpp) REVERT: C 728 MET cc_start: 0.9035 (mmm) cc_final: 0.8659 (mmt) REVERT: D 129 ASN cc_start: 0.8376 (t0) cc_final: 0.7842 (t0) REVERT: E 24 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.7751 (tpp-160) REVERT: E 292 ASN cc_start: 0.7221 (m-40) cc_final: 0.6807 (m-40) REVERT: E 304 ASP cc_start: 0.8318 (m-30) cc_final: 0.8063 (m-30) REVERT: E 358 MET cc_start: 0.9001 (pp-130) cc_final: 0.8768 (tmm) REVERT: E 679 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8354 (p) REVERT: E 769 MET cc_start: 0.9204 (mtm) cc_final: 0.8978 (mtt) REVERT: F 129 ASN cc_start: 0.8178 (t0) cc_final: 0.7675 (t0) REVERT: F 155 GLU cc_start: 0.7808 (tp30) cc_final: 0.7203 (tp30) outliers start: 74 outliers final: 26 residues processed: 318 average time/residue: 0.9245 time to fit residues: 344.1190 Evaluate side-chains 253 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 485 HIS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 646 PHE Chi-restraints excluded: chain C residue 707 ASP Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 377 TYR Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 730 SER Chi-restraints excluded: chain E residue 732 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 129 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 231 optimal weight: 0.8980 chunk 189 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 215 optimal weight: 0.6980 chunk 172 optimal weight: 0.1980 chunk 113 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 209 HIS ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 ASN A 691 ASN B 160 GLN C 188 ASN C 261 GLN ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN C 577 GLN C 607 GLN E 283 ASN ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.094991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.074786 restraints weight = 32093.257| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.65 r_work: 0.2873 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 1.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 19464 Z= 0.202 Angle : 0.680 13.535 26514 Z= 0.350 Chirality : 0.047 0.218 2952 Planarity : 0.005 0.056 3456 Dihedral : 5.247 48.956 2726 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.50 % Allowed : 23.72 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.17), residues: 2517 helix: 0.52 (0.23), residues: 495 sheet: -0.58 (0.21), residues: 633 loop : -0.10 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 152 HIS 0.075 0.003 HIS C 485 PHE 0.013 0.002 PHE A 36 TYR 0.036 0.002 TYR C 319 ARG 0.010 0.001 ARG C 542 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 741) hydrogen bonds : angle 5.96829 ( 2196) covalent geometry : bond 0.00463 (19464) covalent geometry : angle 0.67954 (26514) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 233 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8591 (mp10) REVERT: A 358 MET cc_start: 0.9205 (pp-130) cc_final: 0.8870 (tmm) REVERT: C 248 MET cc_start: 0.9164 (tpp) cc_final: 0.8712 (tpp) REVERT: C 613 THR cc_start: 0.9015 (p) cc_final: 0.8796 (t) REVERT: C 646 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7362 (p90) REVERT: D 129 ASN cc_start: 0.8442 (t0) cc_final: 0.8022 (t0) REVERT: E 24 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.7595 (tpp-160) REVERT: E 171 SER cc_start: 0.8908 (t) cc_final: 0.8660 (m) REVERT: E 173 ILE cc_start: 0.8477 (mt) cc_final: 0.8170 (mt) REVERT: E 358 MET cc_start: 0.8832 (pp-130) cc_final: 0.8553 (tmm) REVERT: E 361 MET cc_start: 0.8906 (tmm) cc_final: 0.8603 (tmm) REVERT: E 402 MET cc_start: 0.9179 (mtp) cc_final: 0.8824 (mtp) REVERT: E 561 ASN cc_start: 0.8439 (t0) cc_final: 0.8209 (t0) REVERT: F 129 ASN cc_start: 0.8331 (t0) cc_final: 0.7720 (t0) REVERT: F 152 ILE cc_start: 0.7950 (mm) cc_final: 0.7684 (mm) REVERT: F 155 GLU cc_start: 0.8203 (tp30) cc_final: 0.7756 (mm-30) outliers start: 70 outliers final: 26 residues processed: 289 average time/residue: 1.0305 time to fit residues: 346.4944 Evaluate side-chains 222 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 646 PHE Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 669 ILE Chi-restraints excluded: chain E residue 732 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 18 optimal weight: 0.5980 chunk 176 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 155 optimal weight: 0.5980 chunk 246 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 ASN B 160 GLN C 80 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS C 261 GLN C 276 HIS ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN E 30 GLN E 124 GLN ** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 HIS F 160 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.091147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.070670 restraints weight = 31613.060| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.64 r_work: 0.2794 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 1.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19464 Z= 0.212 Angle : 0.666 14.521 26514 Z= 0.344 Chirality : 0.047 0.160 2952 Planarity : 0.005 0.047 3456 Dihedral : 5.241 49.172 2726 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.25 % Allowed : 23.77 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2517 helix: 0.38 (0.23), residues: 513 sheet: -0.59 (0.21), residues: 627 loop : -0.02 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 184 HIS 0.013 0.002 HIS C 485 PHE 0.013 0.002 PHE F 126 TYR 0.029 0.002 TYR E 319 ARG 0.009 0.001 ARG E 724 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 741) hydrogen bonds : angle 5.93324 ( 2196) covalent geometry : bond 0.00487 (19464) covalent geometry : angle 0.66593 (26514) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 196 time to evaluate : 2.139 Fit side-chains revert: symmetry clash REVERT: A 111 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8640 (mp10) REVERT: A 358 MET cc_start: 0.9215 (pp-130) cc_final: 0.8881 (tmm) REVERT: B 163 ARG cc_start: 0.8438 (mtp85) cc_final: 0.8172 (mtp85) REVERT: C 248 MET cc_start: 0.9227 (tpp) cc_final: 0.8790 (tpp) REVERT: C 255 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.7900 (mpp) REVERT: C 319 TYR cc_start: 0.8733 (m-80) cc_final: 0.8427 (m-80) REVERT: C 485 HIS cc_start: 0.9405 (OUTLIER) cc_final: 0.9136 (m90) REVERT: C 613 THR cc_start: 0.9069 (p) cc_final: 0.8861 (t) REVERT: D 129 ASN cc_start: 0.8494 (t0) cc_final: 0.8112 (t0) REVERT: E 24 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.7530 (tpp-160) REVERT: E 111 GLN cc_start: 0.8068 (mp10) cc_final: 0.7836 (mp10) REVERT: E 173 ILE cc_start: 0.8552 (mt) cc_final: 0.8285 (mt) REVERT: E 276 HIS cc_start: 0.9085 (OUTLIER) cc_final: 0.7605 (t70) REVERT: E 402 MET cc_start: 0.9175 (mtp) cc_final: 0.8682 (mtp) REVERT: E 561 ASN cc_start: 0.8804 (t0) cc_final: 0.8590 (t0) REVERT: E 644 THR cc_start: 0.7383 (p) cc_final: 0.7175 (t) REVERT: E 669 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8255 (tp) REVERT: F 129 ASN cc_start: 0.8285 (t0) cc_final: 0.7970 (t0) REVERT: F 152 ILE cc_start: 0.8068 (mm) cc_final: 0.7826 (mm) REVERT: F 155 GLU cc_start: 0.8333 (tp30) cc_final: 0.8019 (mm-30) outliers start: 65 outliers final: 26 residues processed: 246 average time/residue: 1.1478 time to fit residues: 323.4430 Evaluate side-chains 203 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 485 HIS Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 276 HIS Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 669 ILE Chi-restraints excluded: chain E residue 732 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 9 optimal weight: 0.7980 chunk 168 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 222 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 HIS ** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 HIS F 130 ASN F 160 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.086557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.067008 restraints weight = 32043.942| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.56 r_work: 0.2719 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 1.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 19464 Z= 0.245 Angle : 0.686 11.863 26514 Z= 0.354 Chirality : 0.048 0.172 2952 Planarity : 0.005 0.048 3456 Dihedral : 5.420 48.997 2726 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.00 % Allowed : 23.47 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.17), residues: 2517 helix: 0.20 (0.23), residues: 531 sheet: -0.60 (0.21), residues: 612 loop : 0.04 (0.18), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 152 HIS 0.011 0.002 HIS C 485 PHE 0.015 0.002 PHE F 126 TYR 0.026 0.002 TYR C 319 ARG 0.008 0.001 ARG E 724 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 741) hydrogen bonds : angle 5.99128 ( 2196) covalent geometry : bond 0.00559 (19464) covalent geometry : angle 0.68634 (26514) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 190 time to evaluate : 2.030 Fit side-chains revert: symmetry clash REVERT: A 111 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8720 (mp10) REVERT: C 37 SER cc_start: 0.8351 (m) cc_final: 0.8041 (p) REVERT: C 144 SER cc_start: 0.8351 (OUTLIER) cc_final: 0.7322 (t) REVERT: C 179 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.7848 (ptmm) REVERT: C 248 MET cc_start: 0.9214 (tpp) cc_final: 0.8744 (tpp) REVERT: C 255 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8121 (mpp) REVERT: C 485 HIS cc_start: 0.9481 (OUTLIER) cc_final: 0.9198 (m90) REVERT: C 613 THR cc_start: 0.9072 (p) cc_final: 0.8871 (t) REVERT: D 129 ASN cc_start: 0.8492 (t0) cc_final: 0.8172 (t0) REVERT: E 24 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.7479 (tpp-160) REVERT: E 111 GLN cc_start: 0.8200 (mp10) cc_final: 0.7937 (mp10) REVERT: E 265 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8452 (p) REVERT: E 402 MET cc_start: 0.9193 (mtp) cc_final: 0.8819 (mtp) REVERT: E 644 THR cc_start: 0.8012 (p) cc_final: 0.7733 (t) REVERT: E 665 GLU cc_start: 0.8336 (mp0) cc_final: 0.7876 (mp0) REVERT: F 155 GLU cc_start: 0.8391 (tp30) cc_final: 0.8096 (mm-30) outliers start: 60 outliers final: 24 residues processed: 233 average time/residue: 1.1627 time to fit residues: 310.4425 Evaluate side-chains 198 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 485 HIS Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain F residue 140 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 150 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 135 optimal weight: 0.0370 chunk 222 optimal weight: 0.8980 chunk 71 optimal weight: 0.0570 chunk 214 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 238 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 245 HIS ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN C 82 GLN C 188 ASN C 276 HIS ** C 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 HIS D 160 GLN ** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.088659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.068871 restraints weight = 31847.924| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.60 r_work: 0.2760 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 1.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19464 Z= 0.176 Angle : 0.630 12.119 26514 Z= 0.325 Chirality : 0.046 0.189 2952 Planarity : 0.005 0.074 3456 Dihedral : 5.198 49.675 2726 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.45 % Allowed : 24.07 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2517 helix: 0.45 (0.23), residues: 513 sheet: -0.57 (0.22), residues: 582 loop : -0.05 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 152 HIS 0.007 0.001 HIS C 485 PHE 0.013 0.001 PHE A 36 TYR 0.021 0.002 TYR E 663 ARG 0.009 0.001 ARG D 163 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 741) hydrogen bonds : angle 5.88410 ( 2196) covalent geometry : bond 0.00410 (19464) covalent geometry : angle 0.63013 (26514) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 1.959 Fit side-chains revert: symmetry clash REVERT: A 111 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8654 (mp10) REVERT: A 234 ARG cc_start: 0.9050 (mtm180) cc_final: 0.8698 (mtm180) REVERT: C 37 SER cc_start: 0.8388 (m) cc_final: 0.8116 (p) REVERT: C 179 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.7794 (ptmm) REVERT: C 248 MET cc_start: 0.9226 (tpp) cc_final: 0.8834 (tpp) REVERT: C 613 THR cc_start: 0.9079 (p) cc_final: 0.8879 (t) REVERT: D 129 ASN cc_start: 0.8465 (t0) cc_final: 0.8167 (t0) REVERT: E 24 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.7475 (tpp-160) REVERT: E 111 GLN cc_start: 0.8116 (mp10) cc_final: 0.7794 (mp10) REVERT: E 248 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7862 (tmm) REVERT: E 250 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.7381 (t80) REVERT: E 276 HIS cc_start: 0.8884 (OUTLIER) cc_final: 0.7293 (t70) REVERT: E 402 MET cc_start: 0.9181 (mtp) cc_final: 0.8842 (mtp) REVERT: E 644 THR cc_start: 0.8090 (p) cc_final: 0.7803 (t) REVERT: E 665 GLU cc_start: 0.8177 (mp0) cc_final: 0.7769 (mp0) REVERT: F 155 GLU cc_start: 0.8350 (tp30) cc_final: 0.8059 (mm-30) REVERT: F 190 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8068 (mt) outliers start: 49 outliers final: 22 residues processed: 219 average time/residue: 1.1255 time to fit residues: 284.4335 Evaluate side-chains 194 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 276 HIS Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 754 THR Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 160 GLN Chi-restraints excluded: chain F residue 190 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 248 optimal weight: 0.5980 chunk 242 optimal weight: 1.9990 chunk 169 optimal weight: 0.3980 chunk 230 optimal weight: 0.0770 chunk 15 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 181 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN C 276 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN E 381 ASN ** E 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.088053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.068279 restraints weight = 31708.289| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 1.59 r_work: 0.2749 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 1.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19464 Z= 0.187 Angle : 0.640 13.557 26514 Z= 0.329 Chirality : 0.047 0.175 2952 Planarity : 0.005 0.071 3456 Dihedral : 5.179 49.816 2726 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.00 % Allowed : 24.72 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2517 helix: 0.41 (0.23), residues: 513 sheet: -0.54 (0.22), residues: 582 loop : -0.06 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 152 HIS 0.007 0.001 HIS E 119 PHE 0.014 0.001 PHE C 36 TYR 0.021 0.002 TYR E 663 ARG 0.011 0.001 ARG D 163 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 741) hydrogen bonds : angle 5.86131 ( 2196) covalent geometry : bond 0.00433 (19464) covalent geometry : angle 0.64025 (26514) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 2.082 Fit side-chains revert: symmetry clash REVERT: A 82 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8709 (mp10) REVERT: A 234 ARG cc_start: 0.9057 (mtm180) cc_final: 0.8706 (mtm180) REVERT: A 358 MET cc_start: 0.9135 (pp-130) cc_final: 0.8899 (tmm) REVERT: C 37 SER cc_start: 0.8435 (m) cc_final: 0.8167 (p) REVERT: C 179 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.7857 (ptmm) REVERT: C 248 MET cc_start: 0.9226 (tpp) cc_final: 0.8795 (tpp) REVERT: C 613 THR cc_start: 0.9088 (p) cc_final: 0.8882 (t) REVERT: D 126 PHE cc_start: 0.8798 (t80) cc_final: 0.8582 (t80) REVERT: D 129 ASN cc_start: 0.8432 (t0) cc_final: 0.8150 (t0) REVERT: D 152 ILE cc_start: 0.7324 (mm) cc_final: 0.6823 (tt) REVERT: E 248 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7842 (tmm) REVERT: E 299 MET cc_start: 0.8630 (tmm) cc_final: 0.8343 (ttp) REVERT: E 402 MET cc_start: 0.9157 (mtp) cc_final: 0.8803 (mtp) REVERT: E 644 THR cc_start: 0.8240 (p) cc_final: 0.7939 (t) REVERT: E 665 GLU cc_start: 0.8156 (mp0) cc_final: 0.7699 (mt-10) REVERT: F 155 GLU cc_start: 0.8267 (tp30) cc_final: 0.7966 (mm-30) REVERT: F 190 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8124 (mt) outliers start: 40 outliers final: 22 residues processed: 205 average time/residue: 1.1081 time to fit residues: 261.3668 Evaluate side-chains 192 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 754 THR Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 190 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 110 optimal weight: 0.6980 chunk 94 optimal weight: 0.0770 chunk 72 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 chunk 157 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN B 171 ASN C 563 GLN D 160 GLN ** E 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.087941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.068240 restraints weight = 31593.205| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 1.59 r_work: 0.2751 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 1.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 19464 Z= 0.186 Angle : 0.641 13.166 26514 Z= 0.328 Chirality : 0.046 0.163 2952 Planarity : 0.005 0.072 3456 Dihedral : 5.182 49.716 2726 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.90 % Allowed : 24.82 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2517 helix: 0.41 (0.23), residues: 513 sheet: -0.54 (0.22), residues: 582 loop : -0.05 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 152 HIS 0.007 0.001 HIS E 119 PHE 0.040 0.002 PHE D 165 TYR 0.022 0.002 TYR E 45 ARG 0.008 0.001 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 741) hydrogen bonds : angle 5.84061 ( 2196) covalent geometry : bond 0.00434 (19464) covalent geometry : angle 0.64145 (26514) =============================================================================== Job complete usr+sys time: 14434.33 seconds wall clock time: 249 minutes 50.22 seconds (14990.22 seconds total)