Starting phenix.real_space_refine on Thu Sep 18 16:57:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d84_46628/09_2025/9d84_46628.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d84_46628/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9d84_46628/09_2025/9d84_46628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d84_46628/09_2025/9d84_46628.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d84_46628/09_2025/9d84_46628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d84_46628/09_2025/9d84_46628.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: C, E, D, F Time building chain proxies: 4.97, per 1000 atoms: 0.26 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: 1.36 Conformation dependent library (CDL) restraints added in 673.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.80 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: 3.09 Time building geometry restraints manager: 1.78 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 15.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.010 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.900 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (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 ARG 0.004 0.001 ARG E 24 TYR 0.018 0.002 TYR E 250 PHE 0.018 0.001 PHE E 5 TRP 0.008 0.001 TRP C 203 HIS 0.006 0.002 HIS E 481 Details of bonding type rmsd covalent geometry : bond 0.00468 (19464) covalent geometry : angle 0.73386 (26514) hydrogen bonds : bond 0.20585 ( 741) hydrogen bonds : angle 8.93646 ( 2196) *********************** 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 : 0.695 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: 0.4559 time to fit residues: 242.2937 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 : 0.657 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.4980 chunk 194 optimal weight: 0.3980 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 247 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 288 GLN A 515 ASN A 577 GLN A 610 ASN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS C 239 ASN C 276 HIS ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 503 ASN ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN D 168 ASN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS E 124 GLN ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN E 283 ASN ** E 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN E 572 ASN E 611 GLN E 622 ASN E 651 HIS E 702 HIS E 761 ASN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.131882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.115789 restraints weight = 32917.719| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.78 r_work: 0.3534 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.7515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 19464 Z= 0.338 Angle : 1.045 21.235 26514 Z= 0.549 Chirality : 0.056 0.368 2952 Planarity : 0.008 0.106 3456 Dihedral : 6.763 54.723 2739 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 6.66 % Allowed : 17.07 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.16), residues: 2517 helix: -0.21 (0.21), residues: 495 sheet: -0.44 (0.20), residues: 642 loop : -0.54 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG C 196 TYR 0.031 0.004 TYR E 601 PHE 0.039 0.003 PHE C 36 TRP 0.027 0.003 TRP C 152 HIS 0.012 0.003 HIS C 481 Details of bonding type rmsd covalent geometry : bond 0.00755 (19464) covalent geometry : angle 1.04477 (26514) hydrogen bonds : bond 0.05446 ( 741) hydrogen bonds : angle 6.73368 ( 2196) *********************** 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 580 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 447 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8446 (tt0) REVERT: A 314 ASP cc_start: 0.8813 (m-30) cc_final: 0.8504 (m-30) REVERT: A 616 THR cc_start: 0.9343 (OUTLIER) cc_final: 0.9127 (p) REVERT: B 181 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: C 17 THR cc_start: 0.6995 (OUTLIER) cc_final: 0.6637 (t) REVERT: C 29 LYS cc_start: 0.7382 (mmtt) cc_final: 0.6689 (mmtt) REVERT: C 192 ASN cc_start: 0.7362 (t0) cc_final: 0.7078 (t0) REVERT: C 223 MET cc_start: 0.7237 (tpp) cc_final: 0.6914 (tpt) REVERT: C 252 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7365 (tt0) REVERT: E 153 ILE cc_start: 0.7553 (mt) cc_final: 0.7163 (mp) REVERT: E 631 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.5836 (mpt) REVERT: E 699 THR cc_start: 0.7478 (OUTLIER) cc_final: 0.7214 (p) REVERT: E 705 MET cc_start: 0.1572 (mmm) cc_final: -0.0587 (tpp) REVERT: F 152 ILE cc_start: 0.6995 (mm) cc_final: 0.6199 (mm) REVERT: F 161 VAL cc_start: 0.7557 (OUTLIER) cc_final: 0.7180 (t) outliers start: 133 outliers final: 25 residues processed: 528 average time/residue: 0.4254 time to fit residues: 262.8499 Evaluate side-chains 325 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 292 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 264 CYS Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 699 THR Chi-restraints excluded: chain E residue 710 VAL Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 205 optimal weight: 0.5980 chunk 134 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 160 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 182 optimal weight: 0.7980 chunk 168 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 GLN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN A 421 ASN A 577 GLN A 597 HIS A 607 GLN A 611 GLN A 714 ASN B 178 GLN C 20 GLN C 30 GLN C 239 ASN C 288 GLN C 337 GLN C 385 GLN C 399 HIS C 421 ASN C 507 GLN ** C 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 HIS C 714 ASN E 82 GLN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 ASN E 337 GLN E 344 GLN E 399 HIS ** E 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 572 ASN E 597 HIS E 651 HIS E 714 ASN F 160 GLN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.104420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.083563 restraints weight = 31498.993| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.74 r_work: 0.3031 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 1.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.124 19464 Z= 0.292 Angle : 0.848 14.903 26514 Z= 0.450 Chirality : 0.052 0.260 2952 Planarity : 0.006 0.074 3456 Dihedral : 5.944 52.849 2730 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 5.41 % Allowed : 19.07 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.16), residues: 2517 helix: 0.25 (0.23), residues: 498 sheet: -0.53 (0.20), residues: 639 loop : -0.22 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 724 TYR 0.033 0.003 TYR C 227 PHE 0.017 0.003 PHE C 5 TRP 0.033 0.003 TRP C 152 HIS 0.016 0.002 HIS C 399 Details of bonding type rmsd covalent geometry : bond 0.00658 (19464) covalent geometry : angle 0.84839 (26514) hydrogen bonds : bond 0.06150 ( 741) hydrogen bonds : angle 6.63329 ( 2196) *********************** 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 417 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 309 time to evaluate : 0.516 Fit side-chains REVERT: A 356 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8958 (mtmm) REVERT: A 753 SER cc_start: 0.9151 (OUTLIER) cc_final: 0.8897 (t) REVERT: C 189 ASP cc_start: 0.7970 (p0) cc_final: 0.7762 (p0) REVERT: C 319 TYR cc_start: 0.7204 (m-80) cc_final: 0.6939 (m-10) REVERT: D 129 ASN cc_start: 0.8357 (t0) cc_final: 0.7913 (t0) REVERT: E 24 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8031 (tpp-160) REVERT: E 215 LYS cc_start: 0.8480 (mtmt) cc_final: 0.8082 (mtmm) REVERT: E 332 MET cc_start: 0.8506 (ptt) cc_final: 0.8185 (ptt) REVERT: E 358 MET cc_start: 0.8703 (ppp) cc_final: 0.8487 (tmm) REVERT: E 430 LEU cc_start: 0.7497 (mt) cc_final: 0.7232 (mm) REVERT: E 679 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8381 (p) REVERT: F 129 ASN cc_start: 0.8102 (t0) cc_final: 0.7723 (t0) REVERT: F 155 GLU cc_start: 0.8279 (tp30) cc_final: 0.7940 (tp30) outliers start: 108 outliers final: 23 residues processed: 380 average time/residue: 0.4986 time to fit residues: 217.1415 Evaluate side-chains 251 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 356 LYS 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 C residue 80 HIS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 646 PHE Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 112 VAL 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 293 CYS Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 730 SER Chi-restraints excluded: chain F residue 154 VAL 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 146 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 118 optimal weight: 0.4980 chunk 106 optimal weight: 0.0470 chunk 94 optimal weight: 0.0670 chunk 241 optimal weight: 0.7980 chunk 147 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 215 optimal weight: 0.7980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 HIS ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN A 611 GLN A 691 ASN C 20 GLN C 261 GLN C 276 HIS C 421 ASN C 515 ASN C 561 ASN C 577 GLN D 130 ASN D 159 GLN ** D 160 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 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 GLN ** E 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 572 ASN E 607 GLN E 622 ASN E 624 GLN E 714 ASN E 740 ASN F 160 GLN F 178 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.099355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.078515 restraints weight = 31346.723| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.70 r_work: 0.2935 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 1.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 19464 Z= 0.168 Angle : 0.629 11.989 26514 Z= 0.329 Chirality : 0.047 0.270 2952 Planarity : 0.005 0.050 3456 Dihedral : 5.404 54.568 2730 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.05 % Allowed : 20.67 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.17), residues: 2517 helix: 0.59 (0.23), residues: 495 sheet: -0.53 (0.20), residues: 633 loop : -0.09 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 724 TYR 0.019 0.002 TYR E 227 PHE 0.012 0.001 PHE A 36 TRP 0.011 0.001 TRP E 203 HIS 0.006 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00384 (19464) covalent geometry : angle 0.62889 (26514) hydrogen bonds : bond 0.03801 ( 741) hydrogen bonds : angle 6.01488 ( 2196) *********************** 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 319 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 238 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 79 VAL cc_start: 0.9174 (t) cc_final: 0.8934 (m) REVERT: B 181 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: C 248 MET cc_start: 0.9200 (tpp) cc_final: 0.8805 (tpp) REVERT: C 260 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8402 (tm-30) REVERT: C 299 MET cc_start: 0.8985 (mtm) cc_final: 0.8702 (ttm) REVERT: C 320 MET cc_start: 0.8012 (tpt) cc_final: 0.7600 (tpt) REVERT: C 322 LYS cc_start: 0.7949 (mmtp) cc_final: 0.7694 (mttm) REVERT: D 129 ASN cc_start: 0.8266 (t0) cc_final: 0.7764 (t0) REVERT: E 24 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.7975 (tpp-160) REVERT: E 171 SER cc_start: 0.8611 (t) cc_final: 0.8263 (m) REVERT: E 173 ILE cc_start: 0.8404 (mt) cc_final: 0.8099 (mt) REVERT: E 299 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.5742 (tpt) REVERT: E 319 TYR cc_start: 0.8956 (m-80) cc_final: 0.8728 (m-80) REVERT: E 358 MET cc_start: 0.8882 (ppp) cc_final: 0.8387 (tmm) REVERT: F 129 ASN cc_start: 0.8197 (t0) cc_final: 0.7672 (t0) REVERT: F 155 GLU cc_start: 0.8310 (tp30) cc_final: 0.7994 (tp30) outliers start: 81 outliers final: 30 residues processed: 292 average time/residue: 0.4833 time to fit residues: 162.7209 Evaluate side-chains 246 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 573 SER Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain E residue 15 ILE 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 250 TYR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 276 HIS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 117 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 145 optimal weight: 0.0770 chunk 128 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 79 optimal weight: 0.0970 chunk 180 optimal weight: 0.4980 chunk 102 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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 385 GLN B 160 GLN C 172 GLN C 209 HIS ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 276 HIS C 371 ASN ** E 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 GLN ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 385 GLN E 516 GLN E 597 HIS E 645 ASN F 160 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.095975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.075361 restraints weight = 31347.459| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.66 r_work: 0.2881 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 1.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 19464 Z= 0.165 Angle : 0.600 12.814 26514 Z= 0.313 Chirality : 0.045 0.161 2952 Planarity : 0.005 0.047 3456 Dihedral : 5.236 54.496 2730 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.65 % Allowed : 20.52 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.17), residues: 2517 helix: 0.74 (0.23), residues: 495 sheet: -0.55 (0.21), residues: 633 loop : -0.04 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 163 TYR 0.017 0.002 TYR E 227 PHE 0.016 0.001 PHE D 128 TRP 0.012 0.001 TRP C 184 HIS 0.044 0.002 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00373 (19464) covalent geometry : angle 0.60008 (26514) hydrogen bonds : bond 0.03731 ( 741) hydrogen bonds : angle 5.84681 ( 2196) *********************** 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 299 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 226 time to evaluate : 0.865 Fit side-chains REVERT: A 79 VAL cc_start: 0.9222 (t) cc_final: 0.9001 (m) REVERT: A 358 MET cc_start: 0.9246 (pp-130) cc_final: 0.8938 (tmm) REVERT: A 655 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.9026 (mmtm) REVERT: B 181 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7958 (mp0) REVERT: C 248 MET cc_start: 0.9261 (tpp) cc_final: 0.8903 (tpp) REVERT: C 255 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7947 (mpp) REVERT: C 299 MET cc_start: 0.9032 (mtm) cc_final: 0.8693 (ttm) REVERT: C 312 THR cc_start: 0.8662 (t) cc_final: 0.8449 (p) REVERT: D 129 ASN cc_start: 0.8333 (t0) cc_final: 0.7750 (t0) REVERT: E 24 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8007 (tpp-160) REVERT: E 171 SER cc_start: 0.8795 (t) cc_final: 0.8541 (m) REVERT: E 173 ILE cc_start: 0.8438 (mt) cc_final: 0.8138 (mt) REVERT: E 199 GLN cc_start: 0.8993 (mm-40) cc_final: 0.8713 (mm-40) REVERT: E 255 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.7676 (mtp) REVERT: E 292 ASN cc_start: 0.7567 (m-40) cc_final: 0.7044 (m-40) REVERT: E 314 ASP cc_start: 0.8909 (m-30) cc_final: 0.8616 (m-30) REVERT: E 358 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8477 (tmm) REVERT: E 402 MET cc_start: 0.9189 (mtp) cc_final: 0.8791 (mtp) REVERT: F 129 ASN cc_start: 0.8296 (t0) cc_final: 0.7707 (t0) REVERT: F 155 GLU cc_start: 0.8291 (tp30) cc_final: 0.7962 (mm-30) outliers start: 73 outliers final: 29 residues processed: 278 average time/residue: 0.4906 time to fit residues: 156.8937 Evaluate side-chains 232 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 655 LYS 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 175 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 600 VAL 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 185 ILE 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 279 ILE Chi-restraints excluded: chain E residue 358 MET Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 161 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 29 optimal weight: 0.5980 chunk 186 optimal weight: 0.9990 chunk 157 optimal weight: 0.0670 chunk 189 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 136 optimal weight: 0.0670 chunk 160 optimal weight: 4.9990 chunk 193 optimal weight: 0.2980 chunk 118 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 226 optimal weight: 0.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- 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 A 283 ASN A 577 GLN A 691 ASN B 160 GLN ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 HIS F 160 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.094064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.073748 restraints weight = 31169.678| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.64 r_work: 0.2852 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 1.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19464 Z= 0.152 Angle : 0.590 14.242 26514 Z= 0.306 Chirality : 0.045 0.144 2952 Planarity : 0.005 0.050 3456 Dihedral : 5.131 55.045 2730 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.25 % Allowed : 20.87 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.17), residues: 2517 helix: 0.88 (0.24), residues: 495 sheet: -0.55 (0.21), residues: 633 loop : -0.00 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 163 TYR 0.025 0.002 TYR C 319 PHE 0.012 0.001 PHE A 36 TRP 0.035 0.001 TRP C 184 HIS 0.006 0.001 HIS C 481 Details of bonding type rmsd covalent geometry : bond 0.00346 (19464) covalent geometry : angle 0.59036 (26514) hydrogen bonds : bond 0.03560 ( 741) hydrogen bonds : angle 5.74674 ( 2196) *********************** 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 277 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 212 time to evaluate : 0.723 Fit side-chains REVERT: A 234 ARG cc_start: 0.9048 (mtm180) cc_final: 0.8828 (mtm110) REVERT: A 358 MET cc_start: 0.9235 (pp-130) cc_final: 0.8924 (tmm) REVERT: A 655 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.9020 (mmtm) REVERT: C 248 MET cc_start: 0.9270 (tpp) cc_final: 0.8829 (tpp) REVERT: C 299 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8581 (ttm) REVERT: C 583 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.8982 (mtt) REVERT: C 689 THR cc_start: 0.9177 (m) cc_final: 0.8910 (t) REVERT: C 707 ASP cc_start: 0.8750 (m-30) cc_final: 0.8468 (m-30) REVERT: D 129 ASN cc_start: 0.8433 (t0) cc_final: 0.7866 (t0) REVERT: E 24 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8015 (tpp-160) REVERT: E 154 GLU cc_start: 0.8460 (tm-30) cc_final: 0.7855 (tm-30) REVERT: E 171 SER cc_start: 0.8905 (t) cc_final: 0.8691 (m) REVERT: E 173 ILE cc_start: 0.8415 (mt) cc_final: 0.8123 (mt) REVERT: E 293 CYS cc_start: 0.6274 (OUTLIER) cc_final: 0.6069 (m) REVERT: E 314 ASP cc_start: 0.9015 (m-30) cc_final: 0.8709 (m-30) REVERT: E 358 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8578 (tmm) REVERT: E 561 ASN cc_start: 0.8568 (t0) cc_final: 0.8337 (t0) REVERT: F 129 ASN cc_start: 0.8348 (t0) cc_final: 0.7702 (t0) REVERT: F 155 GLU cc_start: 0.8130 (tp30) cc_final: 0.7902 (mm-30) outliers start: 65 outliers final: 32 residues processed: 259 average time/residue: 0.5222 time to fit residues: 155.1376 Evaluate side-chains 227 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 655 LYS 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 175 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 217 LEU 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 554 LYS Chi-restraints excluded: chain C residue 573 SER Chi-restraints excluded: chain C residue 583 MET Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 133 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 250 TYR Chi-restraints excluded: chain E residue 276 HIS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 293 CYS Chi-restraints excluded: chain E residue 358 MET Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 234 optimal weight: 0.0980 chunk 78 optimal weight: 0.5980 chunk 101 optimal weight: 0.5980 chunk 176 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 206 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 577 GLN B 160 GLN ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN C 577 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.088125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.068544 restraints weight = 31849.020| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.57 r_work: 0.2760 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 1.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19464 Z= 0.207 Angle : 0.636 15.257 26514 Z= 0.328 Chirality : 0.047 0.162 2952 Planarity : 0.005 0.045 3456 Dihedral : 5.401 53.486 2730 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.00 % Allowed : 20.82 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.17), residues: 2517 helix: 0.57 (0.23), residues: 513 sheet: -0.55 (0.21), residues: 633 loop : 0.10 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 163 TYR 0.024 0.002 TYR C 319 PHE 0.030 0.002 PHE D 165 TRP 0.046 0.002 TRP C 184 HIS 0.007 0.001 HIS C 481 Details of bonding type rmsd covalent geometry : bond 0.00473 (19464) covalent geometry : angle 0.63638 (26514) hydrogen bonds : bond 0.03916 ( 741) hydrogen bonds : angle 5.88125 ( 2196) *********************** 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 245 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 185 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 111 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8662 (mp10) REVERT: C 248 MET cc_start: 0.9293 (tpp) cc_final: 0.8960 (tpp) REVERT: C 299 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8532 (ttm) REVERT: C 583 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.8937 (mtt) REVERT: D 129 ASN cc_start: 0.8481 (t0) cc_final: 0.7965 (t0) REVERT: E 24 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.7973 (tpp-160) REVERT: E 358 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8769 (tmm) REVERT: E 402 MET cc_start: 0.9226 (mtp) cc_final: 0.8848 (mtp) REVERT: F 129 ASN cc_start: 0.8297 (t0) cc_final: 0.8024 (t0) REVERT: F 155 GLU cc_start: 0.8303 (tp30) cc_final: 0.7994 (mm-30) outliers start: 60 outliers final: 24 residues processed: 232 average time/residue: 0.5593 time to fit residues: 147.6798 Evaluate side-chains 197 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 217 LEU 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 554 LYS Chi-restraints excluded: chain C residue 583 MET Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 50 ASP 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 358 MET Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 28 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 167 optimal weight: 0.0980 chunk 126 optimal weight: 0.2980 chunk 215 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 211 optimal weight: 0.9980 chunk 107 optimal weight: 0.0870 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 B 160 GLN ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 ASN C 529 ASN C 577 GLN D 160 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 HIS F 130 ASN F 160 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.089677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.069884 restraints weight = 31518.165| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.60 r_work: 0.2778 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 1.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19464 Z= 0.160 Angle : 0.601 14.779 26514 Z= 0.309 Chirality : 0.045 0.164 2952 Planarity : 0.005 0.047 3456 Dihedral : 5.229 54.171 2730 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.50 % Allowed : 21.62 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.17), residues: 2517 helix: 0.68 (0.23), residues: 513 sheet: -0.54 (0.21), residues: 633 loop : 0.13 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 163 TYR 0.018 0.002 TYR E 227 PHE 0.020 0.001 PHE D 165 TRP 0.023 0.001 TRP C 184 HIS 0.005 0.001 HIS C 481 Details of bonding type rmsd covalent geometry : bond 0.00366 (19464) covalent geometry : angle 0.60054 (26514) hydrogen bonds : bond 0.03615 ( 741) hydrogen bonds : angle 5.80526 ( 2196) *********************** 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 232 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 182 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 111 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8556 (mp10) REVERT: C 248 MET cc_start: 0.9246 (tpp) cc_final: 0.8907 (tpp) REVERT: C 299 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8411 (ttm) REVERT: C 583 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.8963 (mtt) REVERT: D 129 ASN cc_start: 0.8289 (t0) cc_final: 0.7877 (t0) REVERT: D 152 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7000 (tt) REVERT: D 155 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8252 (mm-30) REVERT: E 24 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.7847 (tpp-160) REVERT: E 103 ASP cc_start: 0.8022 (m-30) cc_final: 0.7229 (p0) REVERT: E 314 ASP cc_start: 0.8985 (m-30) cc_final: 0.8671 (m-30) REVERT: F 155 GLU cc_start: 0.8131 (tp30) cc_final: 0.7817 (mm-30) outliers start: 50 outliers final: 27 residues processed: 219 average time/residue: 0.5533 time to fit residues: 138.5167 Evaluate side-chains 193 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 163 GLU 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 175 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 217 LEU 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 554 LYS Chi-restraints excluded: chain C residue 583 MET Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain D residue 152 ILE 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 265 SER Chi-restraints excluded: chain E residue 276 HIS 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 160 GLN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 103 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 221 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 189 optimal weight: 0.6980 chunk 209 optimal weight: 0.0470 chunk 167 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 HIS B 160 GLN ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 HIS C 529 ASN C 563 GLN C 577 GLN D 160 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3176 r_free = 0.3176 target = 0.087318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.067967 restraints weight = 31944.204| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.55 r_work: 0.2742 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 1.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 19464 Z= 0.196 Angle : 0.630 14.474 26514 Z= 0.324 Chirality : 0.046 0.161 2952 Planarity : 0.005 0.077 3456 Dihedral : 5.348 53.716 2730 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.65 % Allowed : 21.47 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.17), residues: 2517 helix: 0.63 (0.23), residues: 513 sheet: -0.54 (0.21), residues: 633 loop : 0.16 (0.18), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 163 TYR 0.026 0.002 TYR C 319 PHE 0.015 0.001 PHE F 128 TRP 0.027 0.001 TRP C 184 HIS 0.013 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00451 (19464) covalent geometry : angle 0.63040 (26514) hydrogen bonds : bond 0.03837 ( 741) hydrogen bonds : angle 5.82918 ( 2196) *********************** 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 224 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 171 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: A 111 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8619 (mp10) REVERT: C 37 SER cc_start: 0.8299 (m) cc_final: 0.8086 (p) REVERT: C 82 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7507 (mp10) REVERT: C 248 MET cc_start: 0.9283 (tpp) cc_final: 0.8962 (tpp) REVERT: C 299 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8503 (ttm) REVERT: C 583 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.8988 (mtt) REVERT: C 692 GLN cc_start: 0.9124 (pt0) cc_final: 0.8918 (pt0) REVERT: D 129 ASN cc_start: 0.8322 (t0) cc_final: 0.7937 (t0) REVERT: D 155 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8180 (mm-30) REVERT: D 189 MET cc_start: 0.8153 (mmt) cc_final: 0.7717 (mmt) REVERT: E 24 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.7842 (tpp-160) REVERT: E 103 ASP cc_start: 0.8052 (m-30) cc_final: 0.7456 (p0) REVERT: E 445 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8380 (mp) REVERT: F 190 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8030 (mt) outliers start: 53 outliers final: 27 residues processed: 211 average time/residue: 0.5107 time to fit residues: 123.9545 Evaluate side-chains 201 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 583 MET Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain D residue 152 ILE 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 265 SER Chi-restraints excluded: chain E residue 276 HIS Chi-restraints excluded: chain E residue 445 LEU 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 140 ILE Chi-restraints excluded: chain F residue 161 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 15 optimal weight: 0.6980 chunk 167 optimal weight: 0.5980 chunk 164 optimal weight: 1.9990 chunk 81 optimal weight: 0.4980 chunk 138 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 165 optimal weight: 0.5980 chunk 105 optimal weight: 0.0020 chunk 93 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 HIS B 160 GLN ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN C 577 GLN D 160 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 ASN F 160 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.088093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.068510 restraints weight = 31402.289| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.57 r_work: 0.2755 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 1.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19464 Z= 0.178 Angle : 0.617 14.092 26514 Z= 0.316 Chirality : 0.046 0.155 2952 Planarity : 0.005 0.072 3456 Dihedral : 5.273 54.154 2730 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.25 % Allowed : 21.47 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.17), residues: 2517 helix: 0.62 (0.23), residues: 513 sheet: -0.57 (0.21), residues: 633 loop : 0.13 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 163 TYR 0.022 0.002 TYR E 45 PHE 0.016 0.001 PHE F 126 TRP 0.025 0.001 TRP C 184 HIS 0.007 0.001 HIS C 481 Details of bonding type rmsd covalent geometry : bond 0.00410 (19464) covalent geometry : angle 0.61715 (26514) hydrogen bonds : bond 0.03729 ( 741) hydrogen bonds : angle 5.82873 ( 2196) ********************** 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 219 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: B 178 GLN cc_start: 0.9215 (mt0) cc_final: 0.8970 (mt0) REVERT: C 82 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7524 (mp10) REVERT: C 248 MET cc_start: 0.9265 (tpp) cc_final: 0.8941 (tpp) REVERT: C 299 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8467 (ttm) REVERT: C 583 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.8996 (mtt) REVERT: D 129 ASN cc_start: 0.8369 (t0) cc_final: 0.8074 (t0) REVERT: D 152 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7008 (tt) REVERT: D 155 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8117 (mm-30) REVERT: D 189 MET cc_start: 0.8151 (mmt) cc_final: 0.7708 (mmt) REVERT: E 24 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.7808 (tpp-160) REVERT: E 103 ASP cc_start: 0.7984 (m-30) cc_final: 0.7493 (p0) REVERT: E 402 MET cc_start: 0.9186 (mtp) cc_final: 0.8881 (mtp) REVERT: E 445 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8253 (mp) REVERT: F 190 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8110 (mt) outliers start: 45 outliers final: 25 residues processed: 207 average time/residue: 0.5111 time to fit residues: 121.3681 Evaluate side-chains 194 residues out of total 2013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 573 SER Chi-restraints excluded: chain C residue 583 MET Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain D residue 152 ILE 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 445 LEU 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 161 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 232 optimal weight: 0.8980 chunk 180 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 101 optimal weight: 0.3980 chunk 241 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 172 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 HIS B 160 GLN ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN C 577 GLN D 160 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.085355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.066532 restraints weight = 32121.174| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 1.52 r_work: 0.2716 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 1.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 19464 Z= 0.213 Angle : 0.641 14.370 26514 Z= 0.329 Chirality : 0.047 0.181 2952 Planarity : 0.005 0.069 3456 Dihedral : 5.436 53.538 2730 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.35 % Allowed : 21.77 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.17), residues: 2517 helix: 0.54 (0.23), residues: 513 sheet: -0.60 (0.21), residues: 633 loop : 0.14 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 163 TYR 0.044 0.002 TYR C 319 PHE 0.019 0.001 PHE C 36 TRP 0.026 0.001 TRP C 184 HIS 0.008 0.001 HIS C 481 Details of bonding type rmsd covalent geometry : bond 0.00490 (19464) covalent geometry : angle 0.64106 (26514) hydrogen bonds : bond 0.03895 ( 741) hydrogen bonds : angle 5.86766 ( 2196) =============================================================================== Job complete usr+sys time: 7212.57 seconds wall clock time: 123 minutes 51.04 seconds (7431.04 seconds total)