Starting phenix.real_space_refine on Mon Jun 16 09:46:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d84_46628/06_2025/9d84_46628.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d84_46628/06_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_46628/06_2025/9d84_46628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d84_46628/06_2025/9d84_46628.map" model { file = "/net/cci-nas-00/data/ceres_data/9d84_46628/06_2025/9d84_46628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d84_46628/06_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-5710/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: 15.53, per 1000 atoms: 0.82 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: 5.03 Conformation dependent library (CDL) restraints added in 2.7 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: 3.35 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: 8.93 Time building geometry restraints manager: 5.97 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: 25.630 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: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 53.410 Find NCS groups from input model: 0.420 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:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.060 ------------------------------------------------------------------------------- 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 : 1.766 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: 1.1262 time to fit residues: 600.1599 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 : 1.861 ------------------------------------------------------------------------------- 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 = 0.140914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.127209 restraints weight = 33383.471| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.75 r_work: 0.3673 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5201 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 50.131 2739 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.52 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 6.39488 ( 2196) covalent geometry : bond 0.00336 (19464) covalent geometry : angle 0.65923 (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 : 2.117 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: 0.7495 (mp10) REVERT: A 144 SER cc_start: 0.8134 (m) cc_final: 0.7863 (p) REVERT: A 224 THR cc_start: 0.7553 (m) cc_final: 0.7339 (m) REVERT: A 250 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7558 (p90) REVERT: A 385 GLN cc_start: 0.6618 (mm-40) cc_final: 0.6318 (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: 0.6654 (Cg_endo) cc_final: 0.6368 (Cg_exo) REVERT: C 296 VAL cc_start: 0.4571 (OUTLIER) cc_final: 0.4192 (p) REVERT: C 365 TYR cc_start: 0.4884 (m-80) cc_final: 0.4637 (m-80) REVERT: F 152 ILE cc_start: 0.5268 (mm) cc_final: 0.4483 (mm) outliers start: 95 outliers final: 17 residues processed: 387 average time/residue: 1.4326 time to fit residues: 653.8217 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 : 3.582 ------------------------------------------------------------------------------- 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: 0.9990 chunk 170 optimal weight: 0.0980 chunk 210 optimal weight: 0.0770 chunk 45 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 214 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 141 optimal weight: 0.4980 chunk 195 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN A 589 ASN A 597 HIS ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN C 172 GLN C 197 ASN C 239 ASN C 276 HIS ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 HIS C 421 ASN D 130 ASN D 168 ASN E 25 HIS ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 390 HIS ** E 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN ** E 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 622 ASN E 702 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.132698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.115925 restraints weight = 32292.130| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.82 r_work: 0.3540 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.8173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 19464 Z= 0.288 Angle : 0.957 19.838 26514 Z= 0.503 Chirality : 0.055 0.403 2952 Planarity : 0.007 0.070 3456 Dihedral : 6.136 55.827 2728 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 6.01 % Allowed : 19.12 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.74 (0.16), residues: 2517 helix: -0.30 (0.22), residues: 501 sheet: -0.56 (0.20), residues: 642 loop : -0.42 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP C 354 HIS 0.015 0.003 HIS C 481 PHE 0.045 0.003 PHE C 569 TYR 0.027 0.003 TYR C 316 ARG 0.016 0.001 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.05687 ( 741) hydrogen bonds : angle 6.73562 ( 2196) covalent geometry : bond 0.00651 (19464) covalent geometry : angle 0.95682 (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 538 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 418 time to evaluate : 1.920 Fit side-chains REVERT: A 144 SER cc_start: 0.8694 (m) cc_final: 0.8477 (p) REVERT: A 314 ASP cc_start: 0.8801 (m-30) cc_final: 0.8461 (m-30) REVERT: A 705 MET cc_start: 0.9300 (mmm) cc_final: 0.9066 (mmm) REVERT: B 189 MET cc_start: 0.8414 (mmm) cc_final: 0.8203 (mmt) REVERT: C 17 THR cc_start: 0.7389 (OUTLIER) cc_final: 0.7014 (t) REVERT: C 192 ASN cc_start: 0.7580 (t0) cc_final: 0.7323 (t0) REVERT: C 223 MET cc_start: 0.7040 (tpp) cc_final: 0.6792 (tpt) REVERT: C 250 TYR cc_start: 0.5486 (OUTLIER) cc_final: 0.5277 (t80) REVERT: C 315 ILE cc_start: 0.7771 (mt) cc_final: 0.7465 (mt) REVERT: C 319 TYR cc_start: 0.6377 (m-80) cc_final: 0.6095 (m-80) REVERT: C 337 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7315 (mt0) REVERT: C 515 ASN cc_start: 0.6873 (m110) cc_final: 0.6570 (m-40) REVERT: C 519 ASN cc_start: 0.7015 (OUTLIER) cc_final: 0.6521 (m110) REVERT: C 663 TYR cc_start: 0.6938 (t80) cc_final: 0.6383 (t80) REVERT: D 129 ASN cc_start: 0.8432 (t0) cc_final: 0.8098 (t0) REVERT: E 163 GLU cc_start: 0.6811 (tm-30) cc_final: 0.6069 (tt0) REVERT: E 250 TYR cc_start: 0.6359 (OUTLIER) cc_final: 0.4884 (t80) REVERT: E 273 ILE cc_start: 0.7308 (mt) cc_final: 0.7081 (mt) REVERT: E 402 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8446 (mtp) REVERT: E 554 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6897 (ptpt) REVERT: E 594 ASP cc_start: 0.6892 (m-30) cc_final: 0.6609 (m-30) REVERT: E 677 VAL cc_start: 0.7498 (t) cc_final: 0.7186 (p) REVERT: E 679 THR cc_start: 0.7927 (OUTLIER) cc_final: 0.7626 (p) REVERT: E 699 THR cc_start: 0.6799 (OUTLIER) cc_final: 0.6521 (p) REVERT: E 705 MET cc_start: 0.4621 (OUTLIER) cc_final: 0.3880 (mmm) REVERT: E 761 ASN cc_start: 0.6940 (m-40) cc_final: 0.6729 (m110) REVERT: F 152 ILE cc_start: 0.6626 (mm) cc_final: 0.5777 (mm) outliers start: 120 outliers final: 24 residues processed: 489 average time/residue: 1.0249 time to fit residues: 582.0928 Evaluate side-chains 331 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 297 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 753 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 46 LYS 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 269 VAL Chi-restraints excluded: chain C residue 337 GLN Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 519 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 E residue 110 ILE Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 377 TYR Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 699 THR Chi-restraints excluded: chain E residue 705 MET Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 176 optimal weight: 0.8980 chunk 196 optimal weight: 0.3980 chunk 130 optimal weight: 0.8980 chunk 236 optimal weight: 1.9990 chunk 159 optimal weight: 0.0870 chunk 194 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 228 optimal weight: 0.0470 chunk 94 optimal weight: 0.9980 overall best weight: 0.3656 ------------------------------------------------------------------------------- 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 199 GLN A 207 GLN A 209 HIS ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN A 529 ASN A 577 GLN A 597 HIS A 607 GLN A 611 GLN B 178 GLN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 ASN C 390 HIS C 424 ASN C 515 ASN C 519 ASN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 GLN ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 390 HIS ** E 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 528 ASN E 529 ASN E 572 ASN ** E 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 HIS E 714 ASN F 160 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.115386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.095390 restraints weight = 31807.859| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.77 r_work: 0.3226 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.9829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 19464 Z= 0.186 Angle : 0.700 14.834 26514 Z= 0.363 Chirality : 0.048 0.299 2952 Planarity : 0.005 0.057 3456 Dihedral : 5.320 56.972 2728 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.95 % Allowed : 23.72 % Favored : 72.32 % 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: 0.16 (0.22), residues: 501 sheet: -0.60 (0.20), residues: 636 loop : -0.18 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 354 HIS 0.012 0.002 HIS E 80 PHE 0.025 0.002 PHE C 559 TYR 0.021 0.002 TYR C 227 ARG 0.009 0.001 ARG C 326 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 741) hydrogen bonds : angle 6.10545 ( 2196) covalent geometry : bond 0.00427 (19464) covalent geometry : angle 0.70013 (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 390 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 311 time to evaluate : 2.159 Fit side-chains REVERT: A 314 ASP cc_start: 0.8926 (m-30) cc_final: 0.8571 (m-30) REVERT: A 358 MET cc_start: 0.9190 (pp-130) cc_final: 0.8823 (tmm) REVERT: A 394 MET cc_start: 0.9309 (tpp) cc_final: 0.8836 (tpp) REVERT: A 769 MET cc_start: 0.9240 (mtt) cc_final: 0.8865 (mtt) REVERT: B 189 MET cc_start: 0.8470 (mmm) cc_final: 0.8142 (mmt) REVERT: C 223 MET cc_start: 0.7891 (tpp) cc_final: 0.7658 (mmm) REVERT: C 239 ASN cc_start: 0.7421 (m-40) cc_final: 0.7218 (m110) REVERT: C 250 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.5854 (t80) REVERT: C 318 GLU cc_start: 0.6282 (tm-30) cc_final: 0.5920 (tm-30) REVERT: C 319 TYR cc_start: 0.7003 (m-80) cc_final: 0.6519 (m-80) REVERT: C 322 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.7127 (mmtp) REVERT: C 365 TYR cc_start: 0.8902 (m-80) cc_final: 0.8532 (m-80) REVERT: C 519 ASN cc_start: 0.7834 (OUTLIER) cc_final: 0.7504 (m110) REVERT: D 129 ASN cc_start: 0.8449 (t0) cc_final: 0.8043 (t0) REVERT: E 5 PHE cc_start: 0.5983 (m-10) cc_final: 0.5775 (m-10) REVERT: E 24 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.7632 (tpp-160) REVERT: E 248 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.6444 (tmm) REVERT: E 277 THR cc_start: 0.4989 (OUTLIER) cc_final: 0.4469 (t) REVERT: E 304 ASP cc_start: 0.7917 (m-30) cc_final: 0.7711 (m-30) REVERT: E 315 ILE cc_start: 0.8148 (mt) cc_final: 0.7453 (mp) REVERT: E 665 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7363 (mm-30) REVERT: E 699 THR cc_start: 0.7199 (p) cc_final: 0.6999 (p) REVERT: E 705 MET cc_start: 0.5872 (OUTLIER) cc_final: 0.5406 (mmm) REVERT: F 129 ASN cc_start: 0.7782 (t0) cc_final: 0.7548 (t0) REVERT: F 152 ILE cc_start: 0.6930 (mm) cc_final: 0.6182 (mm) REVERT: F 155 GLU cc_start: 0.7668 (tp30) cc_final: 0.6843 (tp30) outliers start: 79 outliers final: 27 residues processed: 367 average time/residue: 0.9772 time to fit residues: 417.5774 Evaluate side-chains 273 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 238 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 364 THR 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 80 HIS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 519 ASN 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 50 ASP Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 LYS Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 665 GLU Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 705 MET 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: 1.9990 chunk 170 optimal weight: 0.5980 chunk 136 optimal weight: 0.9980 chunk 242 optimal weight: 1.9990 chunk 222 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 217 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 529 ASN A 572 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 ASN C 519 ASN C 529 ASN E 82 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 GLN E 245 HIS E 283 ASN ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 514 ASN ** E 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 622 ASN E 624 GLN E 761 ASN ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.094876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.073613 restraints weight = 31481.605| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.69 r_work: 0.2844 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 1.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 19464 Z= 0.286 Angle : 0.775 13.387 26514 Z= 0.403 Chirality : 0.051 0.280 2952 Planarity : 0.006 0.080 3456 Dihedral : 5.709 50.173 2728 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.80 % Allowed : 22.57 % Favored : 73.62 % 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: -0.46 (0.17), residues: 2517 helix: 0.12 (0.22), residues: 516 sheet: -0.63 (0.21), residues: 633 loop : -0.17 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 354 HIS 0.011 0.002 HIS C 245 PHE 0.024 0.002 PHE C 520 TYR 0.020 0.003 TYR A 227 ARG 0.020 0.001 ARG C 271 Details of bonding type rmsd hydrogen bonds : bond 0.04514 ( 741) hydrogen bonds : angle 6.20507 ( 2196) covalent geometry : bond 0.00654 (19464) covalent geometry : angle 0.77456 (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 319 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 243 time to evaluate : 1.927 Fit side-chains revert: symmetry clash REVERT: A 753 SER cc_start: 0.9196 (OUTLIER) cc_final: 0.8947 (t) REVERT: A 769 MET cc_start: 0.9335 (mtt) cc_final: 0.8928 (mtt) REVERT: B 189 MET cc_start: 0.8748 (mmm) cc_final: 0.8547 (mmt) REVERT: C 248 MET cc_start: 0.8890 (tpp) cc_final: 0.8594 (tpp) REVERT: C 618 THR cc_start: 0.9034 (m) cc_final: 0.8808 (p) REVERT: D 129 ASN cc_start: 0.8423 (t0) cc_final: 0.7938 (t0) REVERT: E 24 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.7440 (tpp-160) REVERT: E 171 SER cc_start: 0.8842 (t) cc_final: 0.8508 (m) REVERT: E 358 MET cc_start: 0.9018 (ppp) cc_final: 0.8790 (tmm) REVERT: E 361 MET cc_start: 0.8929 (tmm) cc_final: 0.8707 (tmm) REVERT: E 402 MET cc_start: 0.9174 (mtp) cc_final: 0.8772 (mtp) REVERT: E 697 THR cc_start: 0.7245 (m) cc_final: 0.7042 (p) REVERT: E 699 THR cc_start: 0.8486 (p) cc_final: 0.8202 (p) REVERT: E 710 VAL cc_start: 0.9205 (m) cc_final: 0.8912 (t) REVERT: E 747 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8306 (mt) REVERT: F 126 PHE cc_start: 0.8152 (t80) cc_final: 0.7893 (t80) REVERT: F 129 ASN cc_start: 0.8262 (t0) cc_final: 0.7654 (t0) REVERT: F 155 GLU cc_start: 0.8406 (tp30) cc_final: 0.8088 (mm-30) outliers start: 76 outliers final: 32 residues processed: 301 average time/residue: 1.0727 time to fit residues: 373.2705 Evaluate side-chains 234 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 492 ILE 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 112 VAL Chi-restraints excluded: chain E residue 133 LYS Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 276 HIS Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 669 ILE Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 129 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 231 optimal weight: 0.5980 chunk 189 optimal weight: 0.0050 chunk 26 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 215 optimal weight: 0.0980 chunk 172 optimal weight: 4.9990 chunk 113 optimal weight: 0.3980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** 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 385 GLN A 529 ASN A 572 ASN A 691 ASN B 160 GLN B 171 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 276 HIS C 597 HIS ** E 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 HIS F 160 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.094664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.074448 restraints weight = 32018.050| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.64 r_work: 0.2863 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 1.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19464 Z= 0.161 Angle : 0.623 13.267 26514 Z= 0.321 Chirality : 0.046 0.171 2952 Planarity : 0.004 0.048 3456 Dihedral : 5.256 51.458 2728 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.75 % Allowed : 23.37 % Favored : 73.87 % 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: 0.61 (0.23), residues: 495 sheet: -0.60 (0.21), residues: 633 loop : -0.07 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 152 HIS 0.006 0.001 HIS E 485 PHE 0.019 0.001 PHE F 126 TYR 0.018 0.002 TYR C 227 ARG 0.007 0.001 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 741) hydrogen bonds : angle 5.99061 ( 2196) covalent geometry : bond 0.00370 (19464) covalent geometry : angle 0.62259 (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 260 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 205 time to evaluate : 1.957 Fit side-chains revert: symmetry clash REVERT: A 111 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8632 (mp10) REVERT: A 358 MET cc_start: 0.9241 (pp-130) cc_final: 0.8953 (tmm) REVERT: A 394 MET cc_start: 0.9393 (tpp) cc_final: 0.8928 (tpp) REVERT: A 769 MET cc_start: 0.9319 (mtt) cc_final: 0.8930 (mtt) REVERT: B 163 ARG cc_start: 0.8662 (mtp85) cc_final: 0.8402 (mtp85) REVERT: B 189 MET cc_start: 0.8735 (mmm) cc_final: 0.8495 (mmt) REVERT: C 196 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8887 (mtp180) REVERT: C 248 MET cc_start: 0.8885 (tpp) cc_final: 0.8655 (tpp) REVERT: C 255 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.7907 (mpp) REVERT: C 646 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.7505 (p90) REVERT: D 129 ASN cc_start: 0.8527 (t0) cc_final: 0.8166 (t0) REVERT: E 24 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.7548 (tpp-160) REVERT: E 133 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6813 (tttt) REVERT: E 358 MET cc_start: 0.8933 (ppp) cc_final: 0.8726 (tmm) REVERT: E 361 MET cc_start: 0.8979 (tmm) cc_final: 0.8773 (tmm) REVERT: E 561 ASN cc_start: 0.8515 (t0) cc_final: 0.8279 (t0) REVERT: E 669 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8299 (tp) REVERT: E 699 THR cc_start: 0.8302 (p) cc_final: 0.8041 (p) REVERT: E 710 VAL cc_start: 0.9267 (m) cc_final: 0.9052 (t) REVERT: F 129 ASN cc_start: 0.8293 (t0) cc_final: 0.7675 (t0) outliers start: 55 outliers final: 20 residues processed: 242 average time/residue: 1.1016 time to fit residues: 309.2125 Evaluate side-chains 212 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 173 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 616 THR 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 133 LYS Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 276 HIS Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 669 ILE Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 18 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 155 optimal weight: 0.3980 chunk 246 optimal weight: 0.5980 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 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 B 171 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 HIS C 288 GLN C 493 ASN ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN E 385 GLN E 597 HIS F 160 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.089451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.069295 restraints weight = 31736.167| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.60 r_work: 0.2764 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 1.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19464 Z= 0.215 Angle : 0.658 11.578 26514 Z= 0.340 Chirality : 0.048 0.231 2952 Planarity : 0.005 0.069 3456 Dihedral : 5.357 49.258 2728 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.10 % Allowed : 22.57 % Favored : 74.32 % 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: -0.16 (0.17), residues: 2517 helix: 0.62 (0.24), residues: 495 sheet: -0.59 (0.21), residues: 630 loop : -0.00 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 152 HIS 0.011 0.001 HIS C 276 PHE 0.015 0.002 PHE C 559 TYR 0.021 0.002 TYR C 319 ARG 0.007 0.001 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 741) hydrogen bonds : angle 5.98403 ( 2196) covalent geometry : bond 0.00495 (19464) covalent geometry : angle 0.65809 (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 255 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 193 time to evaluate : 1.887 Fit side-chains revert: symmetry clash REVERT: A 111 GLN cc_start: 0.8954 (mm-40) cc_final: 0.8699 (mp10) REVERT: A 360 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8936 (ttt) REVERT: A 769 MET cc_start: 0.9334 (mtt) cc_final: 0.8938 (mtt) REVERT: B 163 ARG cc_start: 0.8477 (mtp85) cc_final: 0.8214 (mtp85) REVERT: C 248 MET cc_start: 0.9031 (tpp) cc_final: 0.8788 (tpp) REVERT: C 445 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8603 (mp) REVERT: D 129 ASN cc_start: 0.8501 (t0) cc_final: 0.8147 (t0) REVERT: E 24 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.7490 (tpp-160) REVERT: E 279 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8077 (tt) REVERT: E 402 MET cc_start: 0.9187 (mtp) cc_final: 0.8825 (mtp) REVERT: F 129 ASN cc_start: 0.8259 (t0) cc_final: 0.7973 (t0) outliers start: 62 outliers final: 25 residues processed: 237 average time/residue: 1.2286 time to fit residues: 333.9194 Evaluate side-chains 197 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 360 MET 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 B residue 173 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain D residue 160 GLN Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 276 HIS Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 9 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 222 optimal weight: 0.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.2980 chunk 105 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** B 160 GLN B 171 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 HIS C 288 GLN C 493 ASN C 607 GLN ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 561 ASN F 130 ASN F 160 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.088175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.067960 restraints weight = 31669.160| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.60 r_work: 0.2739 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 1.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 19464 Z= 0.210 Angle : 0.640 11.301 26514 Z= 0.330 Chirality : 0.047 0.175 2952 Planarity : 0.005 0.048 3456 Dihedral : 5.348 49.105 2728 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.90 % Allowed : 22.57 % Favored : 74.52 % 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: -0.15 (0.17), residues: 2517 helix: 0.51 (0.23), residues: 513 sheet: -0.66 (0.21), residues: 633 loop : 0.09 (0.18), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 184 HIS 0.011 0.001 HIS C 276 PHE 0.014 0.002 PHE F 126 TYR 0.028 0.002 TYR C 319 ARG 0.006 0.001 ARG D 163 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 741) hydrogen bonds : angle 5.96467 ( 2196) covalent geometry : bond 0.00484 (19464) covalent geometry : angle 0.63993 (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 236 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 178 time to evaluate : 2.072 Fit side-chains revert: symmetry clash REVERT: A 111 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8722 (mp10) REVERT: A 234 ARG cc_start: 0.9086 (mtm180) cc_final: 0.8749 (mtm180) REVERT: A 358 MET cc_start: 0.9208 (pp-130) cc_final: 0.8909 (tmm) REVERT: A 769 MET cc_start: 0.9342 (mtt) cc_final: 0.8950 (mtt) REVERT: B 163 ARG cc_start: 0.8484 (mtp85) cc_final: 0.8222 (mtp85) REVERT: C 248 MET cc_start: 0.9054 (tpp) cc_final: 0.8822 (tpp) REVERT: C 299 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7620 (ttp) REVERT: C 445 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8553 (mp) REVERT: D 129 ASN cc_start: 0.8472 (t0) cc_final: 0.8137 (t0) REVERT: D 155 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8513 (mm-30) REVERT: E 279 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.8018 (tt) REVERT: E 402 MET cc_start: 0.9180 (mtp) cc_final: 0.8936 (mtp) REVERT: E 665 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7953 (mt-10) REVERT: F 190 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8015 (mt) outliers start: 58 outliers final: 26 residues processed: 219 average time/residue: 1.1900 time to fit residues: 298.8911 Evaluate side-chains 196 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 616 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 276 HIS Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 644 THR Chi-restraints excluded: chain E residue 732 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 150 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 135 optimal weight: 0.0270 chunk 222 optimal weight: 0.9980 chunk 71 optimal weight: 0.0060 chunk 214 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 238 optimal weight: 0.0970 chunk 76 optimal weight: 0.6980 overall best weight: 0.2252 ------------------------------------------------------------------------------- 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 577 GLN A 611 GLN B 160 GLN B 171 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 ASN ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 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 = 0.3242 r_free = 0.3242 target = 0.091555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.072220 restraints weight = 32070.668| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.59 r_work: 0.2824 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 1.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19464 Z= 0.131 Angle : 0.594 11.814 26514 Z= 0.305 Chirality : 0.045 0.148 2952 Planarity : 0.005 0.072 3456 Dihedral : 5.031 50.525 2728 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.95 % Allowed : 23.87 % Favored : 74.17 % 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: -0.13 (0.17), residues: 2517 helix: 0.69 (0.23), residues: 495 sheet: -0.68 (0.21), residues: 633 loop : 0.05 (0.18), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 152 HIS 0.010 0.001 HIS C 276 PHE 0.015 0.001 PHE F 126 TYR 0.021 0.001 TYR C 319 ARG 0.006 0.001 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.03491 ( 741) hydrogen bonds : angle 5.81690 ( 2196) covalent geometry : bond 0.00301 (19464) covalent geometry : angle 0.59380 (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 230 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 1.932 Fit side-chains REVERT: A 82 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8694 (mp10) REVERT: A 111 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8674 (mp10) REVERT: A 234 ARG cc_start: 0.9025 (mtm180) cc_final: 0.8730 (mtm110) REVERT: A 358 MET cc_start: 0.9165 (pp-130) cc_final: 0.8843 (tmm) REVERT: A 592 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7759 (mtt180) REVERT: A 769 MET cc_start: 0.9297 (mtt) cc_final: 0.8892 (mtt) REVERT: B 163 ARG cc_start: 0.8436 (mtp85) cc_final: 0.8071 (mtp85) REVERT: B 178 GLN cc_start: 0.9144 (mt0) cc_final: 0.8884 (mt0) REVERT: C 37 SER cc_start: 0.8278 (m) cc_final: 0.7927 (p) REVERT: C 299 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7452 (ttp) REVERT: D 129 ASN cc_start: 0.8464 (t0) cc_final: 0.8161 (t0) REVERT: D 155 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8437 (mm-30) REVERT: E 255 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8093 (mtp) REVERT: E 299 MET cc_start: 0.7840 (tmm) cc_final: 0.7500 (ttm) REVERT: E 665 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7879 (mt-10) REVERT: E 765 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8291 (mt-10) REVERT: F 190 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7887 (mt) outliers start: 39 outliers final: 18 residues processed: 222 average time/residue: 1.3184 time to fit residues: 336.3723 Evaluate side-chains 193 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 250 TYR Chi-restraints excluded: chain C residue 276 HIS Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 255 MET Chi-restraints excluded: chain E residue 276 HIS Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 644 THR Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 765 GLU 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 248 optimal weight: 1.9990 chunk 242 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 233 optimal weight: 0.5980 chunk 179 optimal weight: 1.9990 chunk 181 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 577 GLN B 160 GLN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 HIS D 160 GLN E 30 GLN ** E 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.085767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.066352 restraints weight = 32043.798| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 1.55 r_work: 0.2707 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 1.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 19464 Z= 0.232 Angle : 0.662 11.622 26514 Z= 0.341 Chirality : 0.048 0.188 2952 Planarity : 0.005 0.068 3456 Dihedral : 5.382 48.583 2728 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.70 % Allowed : 24.32 % Favored : 73.97 % 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: -0.22 (0.17), residues: 2517 helix: 0.18 (0.22), residues: 537 sheet: -0.62 (0.21), residues: 630 loop : 0.12 (0.18), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 152 HIS 0.014 0.002 HIS C 276 PHE 0.017 0.002 PHE F 126 TYR 0.052 0.002 TYR C 319 ARG 0.010 0.001 ARG E 325 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 741) hydrogen bonds : angle 5.97152 ( 2196) covalent geometry : bond 0.00539 (19464) covalent geometry : angle 0.66159 (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 209 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 2.245 Fit side-chains REVERT: A 82 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8680 (mp10) REVERT: A 111 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8750 (mp10) REVERT: A 234 ARG cc_start: 0.9058 (mtm180) cc_final: 0.8754 (mtm180) REVERT: A 358 MET cc_start: 0.9216 (pp-130) cc_final: 0.8964 (tmm) REVERT: A 769 MET cc_start: 0.9340 (mtt) cc_final: 0.8930 (mtt) REVERT: B 163 ARG cc_start: 0.8409 (mtp85) cc_final: 0.8117 (mtp85) REVERT: B 178 GLN cc_start: 0.9198 (mt0) cc_final: 0.8890 (mt0) REVERT: C 37 SER cc_start: 0.8306 (m) cc_final: 0.8046 (p) REVERT: C 299 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7701 (ttp) REVERT: C 445 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8729 (mp) REVERT: D 129 ASN cc_start: 0.8393 (t0) cc_final: 0.8110 (t0) REVERT: D 155 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8490 (mm-30) REVERT: E 255 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8452 (mtt) REVERT: E 402 MET cc_start: 0.9196 (mtp) cc_final: 0.8750 (mtp) REVERT: F 190 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8006 (mt) outliers start: 34 outliers final: 16 residues processed: 200 average time/residue: 1.2462 time to fit residues: 284.5064 Evaluate side-chains 188 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 180 THR Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 255 MET Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 644 THR Chi-restraints excluded: chain E residue 710 VAL Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain F residue 154 VAL 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: 0.0870 chunk 94 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 126 optimal weight: 0.0980 chunk 90 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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** B 160 GLN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN ** E 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.087787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.068130 restraints weight = 31600.663| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 1.58 r_work: 0.2745 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 1.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19464 Z= 0.178 Angle : 0.624 11.469 26514 Z= 0.320 Chirality : 0.046 0.156 2952 Planarity : 0.005 0.067 3456 Dihedral : 5.231 49.610 2728 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.50 % Allowed : 24.42 % Favored : 74.07 % 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: -0.13 (0.17), residues: 2517 helix: 0.43 (0.23), residues: 513 sheet: -0.63 (0.21), residues: 630 loop : 0.14 (0.18), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 152 HIS 0.015 0.001 HIS C 276 PHE 0.017 0.001 PHE F 126 TYR 0.015 0.002 TYR E 416 ARG 0.009 0.001 ARG E 325 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 741) hydrogen bonds : angle 5.90042 ( 2196) covalent geometry : bond 0.00410 (19464) covalent geometry : angle 0.62442 (26514) =============================================================================== Job complete usr+sys time: 16540.23 seconds wall clock time: 289 minutes 17.55 seconds (17357.55 seconds total)