Starting phenix.real_space_refine on Thu Mar 5 02:41:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tw0_26146/03_2026/7tw0_26146.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tw0_26146/03_2026/7tw0_26146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tw0_26146/03_2026/7tw0_26146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tw0_26146/03_2026/7tw0_26146.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tw0_26146/03_2026/7tw0_26146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tw0_26146/03_2026/7tw0_26146.map" } resolution = 4.6 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.003 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 72 5.16 5 C 11859 2.51 5 N 3084 2.21 5 O 3251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18266 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 6435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6435 Classifications: {'peptide': 814} Link IDs: {'PTRANS': 49, 'TRANS': 764} Chain breaks: 3 Chain: "A" Number of atoms: 6563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6563 Classifications: {'peptide': 830} Link IDs: {'PTRANS': 49, 'TRANS': 780} Chain breaks: 3 Chain: "E" Number of atoms: 5240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5240 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 31, 'TRANS': 633} Chain breaks: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.86, per 1000 atoms: 0.21 Number of scatterers: 18266 At special positions: 0 Unit cell: (95.7, 149.6, 210.1, 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 72 16.00 O 3251 8.00 N 3084 7.00 C 11859 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 Links applied NAG-ASN " NAG A1000 " - " ASN A 642 " " NAG B1000 " - " ASN B 642 " Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 666.6 milliseconds 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4324 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 21 sheets defined 49.5% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 127 through 142 Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 149 through 158 removed outlier: 3.640A pdb=" N ARG B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.787A pdb=" N GLU B 291 " --> pdb=" O THR B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 303 through 317 removed outlier: 4.103A pdb=" N LEU B 307 " --> pdb=" O SER B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 334 Processing helix chain 'B' and resid 335 through 349 removed outlier: 3.610A pdb=" N ARG B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 349 " --> pdb=" O ARG B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 390 removed outlier: 3.565A pdb=" N VAL B 383 " --> pdb=" O PHE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 399 Processing helix chain 'B' and resid 402 through 431 removed outlier: 3.851A pdb=" N LEU B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'B' and resid 436 through 455 removed outlier: 4.162A pdb=" N LEU B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 451 " --> pdb=" O GLN B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 483 removed outlier: 3.532A pdb=" N LEU B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 507 removed outlier: 3.913A pdb=" N TRP B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 516 removed outlier: 3.902A pdb=" N PHE B 511 " --> pdb=" O GLU B 508 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU B 512 " --> pdb=" O GLY B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 547 removed outlier: 3.932A pdb=" N GLN B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 593 removed outlier: 3.898A pdb=" N ASN B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 608 removed outlier: 3.659A pdb=" N PHE B 608 " --> pdb=" O VAL B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 624 Processing helix chain 'B' and resid 660 through 667 Processing helix chain 'B' and resid 667 through 690 removed outlier: 3.985A pdb=" N ALA B 671 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 695 removed outlier: 3.620A pdb=" N LYS B 695 " --> pdb=" O PRO B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 720 Processing helix chain 'B' and resid 727 through 738 Processing helix chain 'B' and resid 760 through 773 removed outlier: 3.630A pdb=" N LEU B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 786 through 799 removed outlier: 3.917A pdb=" N GLY B 790 " --> pdb=" O ALA B 786 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 791 " --> pdb=" O VAL B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 812 removed outlier: 3.780A pdb=" N ASP B 807 " --> pdb=" O ILE B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 827 removed outlier: 3.836A pdb=" N LYS B 826 " --> pdb=" O VAL B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 853 Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 858 through 872 removed outlier: 3.925A pdb=" N VAL B 862 " --> pdb=" O ALA B 858 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 863 " --> pdb=" O LEU B 859 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL B 867 " --> pdb=" O LEU B 863 " (cutoff:3.500A) Proline residue: B 868 - end of helix removed outlier: 3.523A pdb=" N ARG B 871 " --> pdb=" O VAL B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 877 Processing helix chain 'B' and resid 879 through 887 Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 103 through 116 removed outlier: 4.120A pdb=" N LYS A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 149 through 157 Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 194 through 201 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 277 through 290 Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 303 through 317 removed outlier: 3.851A pdb=" N LEU A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 335 removed outlier: 3.618A pdb=" N LEU A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 347 Processing helix chain 'A' and resid 379 through 390 removed outlier: 3.535A pdb=" N VAL A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 402 through 431 removed outlier: 3.826A pdb=" N LEU A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 436 through 455 removed outlier: 3.637A pdb=" N LEU A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 483 removed outlier: 3.575A pdb=" N LEU A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 507 removed outlier: 3.829A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 517 through 547 removed outlier: 3.865A pdb=" N GLN A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 593 removed outlier: 3.679A pdb=" N LEU A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 removed outlier: 3.642A pdb=" N PHE A 608 " --> pdb=" O VAL A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 624 Processing helix chain 'A' and resid 660 through 667 removed outlier: 3.668A pdb=" N MET A 664 " --> pdb=" O PRO A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 690 removed outlier: 3.692A pdb=" N ALA A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 719 Processing helix chain 'A' and resid 727 through 738 Processing helix chain 'A' and resid 760 through 773 Processing helix chain 'A' and resid 776 through 781 removed outlier: 3.668A pdb=" N LEU A 780 " --> pdb=" O MET A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 799 removed outlier: 4.204A pdb=" N LEU A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 812 removed outlier: 3.665A pdb=" N ASP A 807 " --> pdb=" O ILE A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.552A pdb=" N HIS A 819 " --> pdb=" O PRO A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 removed outlier: 3.843A pdb=" N LYS A 826 " --> pdb=" O VAL A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 853 Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 858 through 872 removed outlier: 4.073A pdb=" N VAL A 867 " --> pdb=" O LEU A 863 " (cutoff:3.500A) Proline residue: A 868 - end of helix Processing helix chain 'A' and resid 873 through 877 Processing helix chain 'A' and resid 879 through 887 Processing helix chain 'E' and resid 13 through 18 Processing helix chain 'E' and resid 52 through 58 removed outlier: 3.615A pdb=" N LYS E 58 " --> pdb=" O PRO E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 159 Processing helix chain 'E' and resid 187 through 197 Processing helix chain 'E' and resid 201 through 206 removed outlier: 4.087A pdb=" N SER E 206 " --> pdb=" O GLU E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 227 removed outlier: 3.745A pdb=" N VAL E 211 " --> pdb=" O GLN E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 248 through 258 Processing helix chain 'E' and resid 269 through 283 removed outlier: 4.497A pdb=" N ALA E 273 " --> pdb=" O TRP E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 374 Processing helix chain 'E' and resid 381 through 390 removed outlier: 3.524A pdb=" N ASN E 390 " --> pdb=" O PHE E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 435 Processing helix chain 'E' and resid 441 through 458 removed outlier: 3.566A pdb=" N LYS E 445 " --> pdb=" O SER E 441 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU E 457 " --> pdb=" O LYS E 453 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 550 through 552 No H-bonds generated for 'chain 'E' and resid 550 through 552' Processing sheet with id=AA1, first strand: chain 'B' and resid 85 through 87 removed outlier: 6.662A pdb=" N LEU B 61 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG B 80 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL B 59 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 118 through 123 removed outlier: 3.618A pdb=" N THR B 118 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 244 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLN B 248 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG B 263 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ALA B 226 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU B 265 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU B 228 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL B 267 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 230 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU B 269 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TYR B 58 " --> pdb=" O THR B 227 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL B 229 " --> pdb=" O TYR B 58 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLU B 60 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL B 231 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLN B 62 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL B 59 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG B 80 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU B 61 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 103 removed outlier: 3.892A pdb=" N LEU B 102 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL A 320 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 319 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 177 through 178 Processing sheet with id=AA5, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AA6, first strand: chain 'B' and resid 739 through 742 removed outlier: 6.924A pdb=" N VAL B 740 " --> pdb=" O GLN B 754 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.685A pdb=" N ALA A 35 " --> pdb=" O ARG E 638 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA E 598 " --> pdb=" O VAL E 685 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 86 through 87 removed outlier: 6.899A pdb=" N LEU A 61 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ARG A 80 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 59 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS A 56 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR A 227 " --> pdb=" O LYS A 56 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR A 58 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL A 229 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLU A 60 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL A 231 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN A 62 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ARG A 263 " --> pdb=" O SER A 224 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA A 226 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 265 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU A 228 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL A 267 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 230 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU A 269 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N PHE A 264 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 10.721A pdb=" N GLU A 249 " --> pdb=" O PHE A 264 " (cutoff:3.500A) removed outlier: 11.842A pdb=" N PHE A 266 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N LEU A 247 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 11.380A pdb=" N LEU A 268 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 12.587A pdb=" N VAL A 245 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL A 119 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ARG A 246 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU A 121 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN A 248 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU A 123 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ALA A 250 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 86 through 87 removed outlier: 6.899A pdb=" N LEU A 61 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ARG A 80 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 59 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AB2, first strand: chain 'A' and resid 739 through 741 Processing sheet with id=AB3, first strand: chain 'E' and resid 7 through 12 removed outlier: 7.108A pdb=" N TYR E 44 " --> pdb=" O LYS E 8 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N CYS E 10 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE E 42 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE E 12 " --> pdb=" O THR E 40 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N THR E 40 " --> pdb=" O PHE E 12 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ARG E 97 " --> pdb=" O SER E 101 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR E 103 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL E 93 " --> pdb=" O SER E 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 32 through 34 removed outlier: 5.564A pdb=" N LEU E 130 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU E 121 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY E 132 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY E 115 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 163 through 168 Processing sheet with id=AB6, first strand: chain 'E' and resid 286 through 295 removed outlier: 6.779A pdb=" N ALA E 286 " --> pdb=" O CYS E 332 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N CYS E 332 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL E 288 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR E 330 " --> pdb=" O VAL E 288 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR E 290 " --> pdb=" O THR E 328 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR E 328 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE E 292 " --> pdb=" O PHE E 326 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE E 326 " --> pdb=" O PHE E 292 " (cutoff:3.500A) removed outlier: 11.401A pdb=" N THR E 328 " --> pdb=" O PRO E 351 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR E 330 " --> pdb=" O LEU E 349 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP E 364 " --> pdb=" O HIS E 350 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 303 through 308 removed outlier: 6.190A pdb=" N ILE E 304 " --> pdb=" O VAL E 394 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N TRP E 396 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLU E 306 " --> pdb=" O TRP E 396 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 408 through 409 removed outlier: 6.512A pdb=" N ASP E 408 " --> pdb=" O PHE E 578 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N GLN E 580 " --> pdb=" O ASP E 408 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU E 485 " --> pdb=" O CYS E 586 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 408 through 409 removed outlier: 6.512A pdb=" N ASP E 408 " --> pdb=" O PHE E 578 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N GLN E 580 " --> pdb=" O ASP E 408 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA E 515 " --> pdb=" O LYS E 525 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LYS E 525 " --> pdb=" O ALA E 515 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 419 through 421 Processing sheet with id=AC2, first strand: chain 'E' and resid 475 through 480 Processing sheet with id=AC3, first strand: chain 'E' and resid 590 through 593 891 hydrogen bonds defined for protein. 2541 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: 3.27 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5056 1.33 - 1.45: 3169 1.45 - 1.57: 10341 1.57 - 1.69: 0 1.69 - 1.81: 119 Bond restraints: 18685 Sorted by residual: bond pdb=" N LEU A 775 " pdb=" CA LEU A 775 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.10e-02 8.26e+03 6.62e+00 bond pdb=" C PRO A 563 " pdb=" O PRO A 563 " ideal model delta sigma weight residual 1.235 1.217 0.018 1.30e-02 5.92e+03 1.94e+00 bond pdb=" C1 NAG B1000 " pdb=" O5 NAG B1000 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.87e+00 bond pdb=" C1 NAG A1000 " pdb=" O5 NAG A1000 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.81e+00 bond pdb=" CG LEU B 540 " pdb=" CD2 LEU B 540 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.76e+00 ... (remaining 18680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 24803 2.01 - 4.02: 463 4.02 - 6.03: 82 6.03 - 8.04: 26 8.04 - 10.05: 12 Bond angle restraints: 25386 Sorted by residual: angle pdb=" N GLU B 218 " pdb=" CA GLU B 218 " pdb=" CB GLU B 218 " ideal model delta sigma weight residual 110.30 115.97 -5.67 1.54e+00 4.22e-01 1.36e+01 angle pdb=" C VAL A 446 " pdb=" N GLN A 447 " pdb=" CA GLN A 447 " ideal model delta sigma weight residual 120.72 114.95 5.77 1.67e+00 3.59e-01 1.20e+01 angle pdb=" C LEU B 217 " pdb=" N GLU B 218 " pdb=" CA GLU B 218 " ideal model delta sigma weight residual 120.68 114.86 5.82 1.70e+00 3.46e-01 1.17e+01 angle pdb=" N PHE B 597 " pdb=" CA PHE B 597 " pdb=" C PHE B 597 " ideal model delta sigma weight residual 108.07 110.99 -2.92 8.90e-01 1.26e+00 1.08e+01 angle pdb=" CB MET B 712 " pdb=" CG MET B 712 " pdb=" SD MET B 712 " ideal model delta sigma weight residual 112.70 122.32 -9.62 3.00e+00 1.11e-01 1.03e+01 ... (remaining 25381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10188 17.95 - 35.89: 865 35.89 - 53.84: 115 53.84 - 71.78: 30 71.78 - 89.73: 20 Dihedral angle restraints: 11218 sinusoidal: 4543 harmonic: 6675 Sorted by residual: dihedral pdb=" CA PRO A 568 " pdb=" C PRO A 568 " pdb=" N ASN A 569 " pdb=" CA ASN A 569 " ideal model delta harmonic sigma weight residual -180.00 -161.03 -18.97 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA TRP B 81 " pdb=" C TRP B 81 " pdb=" N VAL B 82 " pdb=" CA VAL B 82 " ideal model delta harmonic sigma weight residual 180.00 163.10 16.90 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA GLN E 225 " pdb=" C GLN E 225 " pdb=" N ARG E 226 " pdb=" CA ARG E 226 " ideal model delta harmonic sigma weight residual -180.00 -163.20 -16.80 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 11215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2440 0.058 - 0.116: 446 0.116 - 0.174: 53 0.174 - 0.232: 4 0.232 - 0.290: 2 Chirality restraints: 2945 Sorted by residual: chirality pdb=" CB ILE E 81 " pdb=" CA ILE E 81 " pdb=" CG1 ILE E 81 " pdb=" CG2 ILE E 81 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB ILE B 783 " pdb=" CA ILE B 783 " pdb=" CG1 ILE B 783 " pdb=" CG2 ILE B 783 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA GLN A 447 " pdb=" N GLN A 447 " pdb=" C GLN A 447 " pdb=" CB GLN A 447 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.07e-01 ... (remaining 2942 not shown) Planarity restraints: 3216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 634 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.12e+00 pdb=" N PRO B 635 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 635 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 635 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 390 " -0.038 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO A 391 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 391 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 391 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 544 " -0.019 2.00e-02 2.50e+03 1.70e-02 5.03e+00 pdb=" CG PHE B 544 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE B 544 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 544 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 544 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 544 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE B 544 " -0.000 2.00e-02 2.50e+03 ... (remaining 3213 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 567 2.72 - 3.26: 17894 3.26 - 3.81: 28591 3.81 - 4.35: 33633 4.35 - 4.90: 58320 Nonbonded interactions: 139005 Sorted by model distance: nonbonded pdb=" O LEU B 863 " pdb=" OG1 THR B 866 " model vdw 2.169 3.040 nonbonded pdb=" O PHE B 679 " pdb=" NE2 GLN B 683 " model vdw 2.186 3.120 nonbonded pdb=" OD2 ASP E 199 " pdb=" NE2 HIS E 210 " model vdw 2.275 3.120 nonbonded pdb=" OD1 ASP B 137 " pdb=" NH1 ARG B 150 " model vdw 2.280 3.120 nonbonded pdb=" O THR A 103 " pdb=" OG SER A 106 " model vdw 2.286 3.040 ... (remaining 139000 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 55 through 1000) selection = (chain 'B' and (resid 55 through 348 or resid 369 through 1000)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.820 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.003 0.044 18687 Z= 0.141 Angle : 0.727 10.055 25392 Z= 0.365 Chirality : 0.044 0.290 2945 Planarity : 0.005 0.057 3214 Dihedral : 13.827 89.727 6894 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.05 % Allowed : 0.25 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.17), residues: 2287 helix: 1.34 (0.17), residues: 1016 sheet: 0.42 (0.29), residues: 323 loop : -1.06 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 80 TYR 0.026 0.001 TYR B 413 PHE 0.038 0.001 PHE B 544 TRP 0.014 0.001 TRP A 831 HIS 0.008 0.001 HIS B 834 Details of bonding type rmsd covalent geometry : bond 0.00277 (18685) covalent geometry : angle 0.72675 (25386) hydrogen bonds : bond 0.13717 ( 879) hydrogen bonds : angle 5.49419 ( 2541) link_NAG-ASN : bond 0.00223 ( 2) link_NAG-ASN : angle 1.08894 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: B 66 MET cc_start: 0.7608 (tmm) cc_final: 0.7330 (tmm) REVERT: B 114 PHE cc_start: 0.9166 (t80) cc_final: 0.8844 (t80) REVERT: B 418 SER cc_start: 0.9069 (t) cc_final: 0.8767 (p) REVERT: B 486 TYR cc_start: 0.6578 (t80) cc_final: 0.5495 (t80) REVERT: B 617 MET cc_start: 0.9137 (mmp) cc_final: 0.8796 (mmm) REVERT: B 712 MET cc_start: 0.7737 (mpp) cc_final: 0.7423 (mpp) REVERT: B 776 MET cc_start: 0.8137 (mtm) cc_final: 0.7896 (mtp) REVERT: B 806 PHE cc_start: 0.8531 (t80) cc_final: 0.8276 (t80) REVERT: B 833 MET cc_start: 0.7424 (mtm) cc_final: 0.7192 (mtm) REVERT: B 874 LEU cc_start: 0.9134 (mm) cc_final: 0.8874 (mt) REVERT: A 31 MET cc_start: 0.2357 (tpt) cc_final: 0.2128 (tpt) REVERT: A 433 ASN cc_start: 0.9284 (m110) cc_final: 0.8805 (t0) REVERT: A 435 MET cc_start: 0.7713 (ptp) cc_final: 0.7078 (pmm) REVERT: A 486 TYR cc_start: 0.7890 (t80) cc_final: 0.7087 (t80) REVERT: A 663 MET cc_start: 0.9387 (tpp) cc_final: 0.9030 (tpp) REVERT: A 752 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7938 (tm-30) REVERT: E 190 ASP cc_start: 0.9166 (m-30) cc_final: 0.8883 (t0) REVERT: E 456 MET cc_start: 0.8253 (mmp) cc_final: 0.7566 (tpt) REVERT: E 618 MET cc_start: 0.8276 (mmp) cc_final: 0.7811 (mmm) REVERT: E 672 MET cc_start: 0.8525 (mmp) cc_final: 0.8321 (mmm) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.1095 time to fit residues: 31.7892 Evaluate side-chains 125 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 HIS ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 HIS ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 HIS A 457 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 517 HIS ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.042272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.030766 restraints weight = 148297.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.031699 restraints weight = 90000.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.032332 restraints weight = 65124.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.032769 restraints weight = 52481.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.033064 restraints weight = 45398.074| |-----------------------------------------------------------------------------| r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 18687 Z= 0.336 Angle : 0.845 12.126 25392 Z= 0.427 Chirality : 0.047 0.226 2945 Planarity : 0.007 0.058 3214 Dihedral : 5.313 55.555 2523 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.40 % Allowed : 7.47 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2287 helix: 0.77 (0.16), residues: 1023 sheet: 0.11 (0.28), residues: 326 loop : -1.20 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 150 TYR 0.025 0.003 TYR B 299 PHE 0.029 0.003 PHE B 591 TRP 0.021 0.003 TRP A 75 HIS 0.015 0.002 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00731 (18685) covalent geometry : angle 0.84452 (25386) hydrogen bonds : bond 0.05810 ( 879) hydrogen bonds : angle 5.31317 ( 2541) link_NAG-ASN : bond 0.00233 ( 2) link_NAG-ASN : angle 2.31754 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: B 289 MET cc_start: 0.7540 (mmp) cc_final: 0.7304 (mmp) REVERT: B 617 MET cc_start: 0.9240 (mmp) cc_final: 0.8910 (mmm) REVERT: B 683 GLN cc_start: 0.8765 (mp-120) cc_final: 0.8504 (mm-40) REVERT: B 696 MET cc_start: 0.6186 (mmm) cc_final: 0.5849 (tpt) REVERT: B 741 MET cc_start: 0.6359 (ppp) cc_final: 0.6120 (ppp) REVERT: B 776 MET cc_start: 0.7901 (mtm) cc_final: 0.7531 (mtp) REVERT: B 806 PHE cc_start: 0.8852 (t80) cc_final: 0.8640 (t80) REVERT: A 31 MET cc_start: 0.2707 (tpt) cc_final: 0.2416 (tpt) REVERT: A 435 MET cc_start: 0.7699 (ptp) cc_final: 0.7345 (pmm) REVERT: A 663 MET cc_start: 0.9379 (tpp) cc_final: 0.9097 (tpp) REVERT: A 683 GLN cc_start: 0.9279 (mm-40) cc_final: 0.8929 (mm110) REVERT: A 752 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7877 (tm-30) REVERT: E 386 PHE cc_start: 0.9294 (t80) cc_final: 0.9019 (t80) REVERT: E 453 LYS cc_start: 0.9557 (mtpp) cc_final: 0.9306 (mmtt) REVERT: E 618 MET cc_start: 0.8123 (mmp) cc_final: 0.7914 (mmm) REVERT: E 648 MET cc_start: 0.6599 (tpt) cc_final: 0.6363 (tpt) outliers start: 8 outliers final: 4 residues processed: 144 average time/residue: 0.1014 time to fit residues: 24.6091 Evaluate side-chains 100 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 84 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 229 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 224 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN B 683 GLN A 192 HIS ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.043563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.032037 restraints weight = 142998.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.032999 restraints weight = 87140.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.033662 restraints weight = 62935.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.034101 restraints weight = 50432.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.034425 restraints weight = 43486.042| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18687 Z= 0.142 Angle : 0.600 8.191 25392 Z= 0.299 Chirality : 0.041 0.233 2945 Planarity : 0.005 0.054 3214 Dihedral : 4.713 57.538 2523 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.17), residues: 2287 helix: 1.34 (0.17), residues: 1032 sheet: 0.28 (0.29), residues: 324 loop : -1.14 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 150 TYR 0.015 0.002 TYR E 413 PHE 0.020 0.001 PHE A 537 TRP 0.017 0.001 TRP A 105 HIS 0.006 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00307 (18685) covalent geometry : angle 0.59990 (25386) hydrogen bonds : bond 0.04595 ( 879) hydrogen bonds : angle 4.71985 ( 2541) link_NAG-ASN : bond 0.00170 ( 2) link_NAG-ASN : angle 1.76976 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 289 MET cc_start: 0.7474 (mmp) cc_final: 0.7237 (mmp) REVERT: B 435 MET cc_start: 0.7840 (tpt) cc_final: 0.7568 (tpp) REVERT: B 617 MET cc_start: 0.9212 (mmp) cc_final: 0.8890 (mmm) REVERT: B 683 GLN cc_start: 0.8545 (mp10) cc_final: 0.8303 (mm-40) REVERT: B 806 PHE cc_start: 0.8712 (t80) cc_final: 0.8445 (t80) REVERT: A 663 MET cc_start: 0.9334 (tpp) cc_final: 0.9075 (tpp) REVERT: A 675 PHE cc_start: 0.8967 (t80) cc_final: 0.8722 (t80) REVERT: A 769 LEU cc_start: 0.9428 (mm) cc_final: 0.9202 (mt) REVERT: A 859 LEU cc_start: 0.9181 (tt) cc_final: 0.8776 (mt) REVERT: E 453 LYS cc_start: 0.9569 (mtpp) cc_final: 0.9314 (mmtt) REVERT: E 618 MET cc_start: 0.7992 (mmp) cc_final: 0.7775 (mmm) REVERT: E 648 MET cc_start: 0.6558 (tpt) cc_final: 0.6342 (tpt) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1099 time to fit residues: 28.9881 Evaluate side-chains 108 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 113 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 218 optimal weight: 20.0000 chunk 191 optimal weight: 2.9990 chunk 214 optimal weight: 9.9990 chunk 19 optimal weight: 0.0370 chunk 1 optimal weight: 6.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 315 ASN E 390 ASN ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.043345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.031730 restraints weight = 145802.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.032715 restraints weight = 88061.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.033397 restraints weight = 63032.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.033856 restraints weight = 50395.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.034137 restraints weight = 43347.181| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18687 Z= 0.186 Angle : 0.631 9.550 25392 Z= 0.313 Chirality : 0.041 0.228 2945 Planarity : 0.005 0.052 3214 Dihedral : 4.755 55.717 2523 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.05 % Allowed : 3.71 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.17), residues: 2287 helix: 1.30 (0.17), residues: 1032 sheet: 0.22 (0.29), residues: 327 loop : -1.12 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 344 TYR 0.018 0.002 TYR E 413 PHE 0.025 0.002 PHE B 544 TRP 0.016 0.002 TRP A 105 HIS 0.006 0.001 HIS E 589 Details of bonding type rmsd covalent geometry : bond 0.00409 (18685) covalent geometry : angle 0.63086 (25386) hydrogen bonds : bond 0.04547 ( 879) hydrogen bonds : angle 4.75957 ( 2541) link_NAG-ASN : bond 0.00189 ( 2) link_NAG-ASN : angle 1.92724 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 289 MET cc_start: 0.7459 (mmp) cc_final: 0.7223 (mmp) REVERT: B 392 TYR cc_start: 0.8404 (m-80) cc_final: 0.8048 (m-80) REVERT: B 435 MET cc_start: 0.7979 (tpt) cc_final: 0.7759 (tpp) REVERT: B 500 LEU cc_start: 0.9411 (mm) cc_final: 0.9193 (mt) REVERT: B 617 MET cc_start: 0.9221 (mmp) cc_final: 0.8915 (mmm) REVERT: B 675 PHE cc_start: 0.9468 (t80) cc_final: 0.9267 (t80) REVERT: B 683 GLN cc_start: 0.8580 (mp10) cc_final: 0.8373 (mm-40) REVERT: B 696 MET cc_start: 0.6118 (mmm) cc_final: 0.5729 (tpt) REVERT: B 806 PHE cc_start: 0.8718 (t80) cc_final: 0.8438 (t80) REVERT: A 31 MET cc_start: 0.3428 (tpt) cc_final: 0.3107 (tpt) REVERT: A 663 MET cc_start: 0.9326 (tpp) cc_final: 0.9039 (tpp) REVERT: A 807 ASP cc_start: 0.8054 (m-30) cc_final: 0.7829 (t70) REVERT: E 453 LYS cc_start: 0.9573 (mtpp) cc_final: 0.9323 (mmtt) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.1092 time to fit residues: 27.1625 Evaluate side-chains 107 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 0.0980 chunk 173 optimal weight: 2.9990 chunk 209 optimal weight: 10.0000 chunk 212 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 GLN E 390 ASN ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.043270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.031735 restraints weight = 145574.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.032721 restraints weight = 88031.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.033379 restraints weight = 63404.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.033818 restraints weight = 50937.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.034122 restraints weight = 44064.752| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18687 Z= 0.184 Angle : 0.632 8.789 25392 Z= 0.316 Chirality : 0.042 0.230 2945 Planarity : 0.005 0.054 3214 Dihedral : 4.818 56.156 2523 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.05 % Allowed : 3.06 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.17), residues: 2287 helix: 1.23 (0.17), residues: 1032 sheet: 0.19 (0.29), residues: 325 loop : -1.08 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 730 TYR 0.017 0.002 TYR E 413 PHE 0.025 0.002 PHE B 544 TRP 0.018 0.002 TRP A 831 HIS 0.006 0.001 HIS E 210 Details of bonding type rmsd covalent geometry : bond 0.00403 (18685) covalent geometry : angle 0.63146 (25386) hydrogen bonds : bond 0.04503 ( 879) hydrogen bonds : angle 4.78353 ( 2541) link_NAG-ASN : bond 0.00210 ( 2) link_NAG-ASN : angle 1.90648 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 289 MET cc_start: 0.7407 (mmp) cc_final: 0.7136 (mmp) REVERT: B 392 TYR cc_start: 0.8407 (m-80) cc_final: 0.8067 (m-80) REVERT: B 617 MET cc_start: 0.9200 (mmp) cc_final: 0.8907 (mmm) REVERT: B 683 GLN cc_start: 0.8486 (mp10) cc_final: 0.8197 (mm-40) REVERT: B 806 PHE cc_start: 0.8763 (t80) cc_final: 0.8490 (t80) REVERT: A 31 MET cc_start: 0.3603 (tpt) cc_final: 0.3310 (tpt) REVERT: A 112 ARG cc_start: 0.7679 (tmm160) cc_final: 0.7429 (ttp80) REVERT: A 663 MET cc_start: 0.9308 (tpp) cc_final: 0.9033 (tpp) REVERT: E 453 LYS cc_start: 0.9574 (mtpp) cc_final: 0.9318 (mmtt) REVERT: E 618 MET cc_start: 0.7813 (mmp) cc_final: 0.7602 (mmm) outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.1013 time to fit residues: 25.3585 Evaluate side-chains 109 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 118 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 223 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 88 optimal weight: 0.9990 chunk 110 optimal weight: 0.0060 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN A 330 GLN A 569 ASN A 683 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 390 ASN ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.043802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.032222 restraints weight = 144030.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.033208 restraints weight = 87021.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.033881 restraints weight = 62618.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.034318 restraints weight = 50241.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.034644 restraints weight = 43378.283| |-----------------------------------------------------------------------------| r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18687 Z= 0.132 Angle : 0.589 7.982 25392 Z= 0.290 Chirality : 0.041 0.234 2945 Planarity : 0.005 0.051 3214 Dihedral : 4.600 58.623 2523 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.05 % Allowed : 2.46 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.18), residues: 2287 helix: 1.48 (0.17), residues: 1027 sheet: 0.30 (0.29), residues: 326 loop : -1.07 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 730 TYR 0.015 0.001 TYR B 413 PHE 0.020 0.001 PHE B 544 TRP 0.022 0.001 TRP A 831 HIS 0.006 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00291 (18685) covalent geometry : angle 0.58808 (25386) hydrogen bonds : bond 0.04150 ( 879) hydrogen bonds : angle 4.58038 ( 2541) link_NAG-ASN : bond 0.00167 ( 2) link_NAG-ASN : angle 1.81686 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 289 MET cc_start: 0.7418 (mmp) cc_final: 0.7168 (mmp) REVERT: B 447 GLN cc_start: 0.8671 (mt0) cc_final: 0.8461 (mt0) REVERT: B 617 MET cc_start: 0.9221 (mmp) cc_final: 0.8892 (mmm) REVERT: B 683 GLN cc_start: 0.8448 (mp10) cc_final: 0.8158 (mm-40) REVERT: B 806 PHE cc_start: 0.8682 (t80) cc_final: 0.8431 (t80) REVERT: A 112 ARG cc_start: 0.7737 (tmm160) cc_final: 0.7513 (ttp80) REVERT: A 663 MET cc_start: 0.9283 (tpp) cc_final: 0.9019 (tpp) REVERT: A 769 LEU cc_start: 0.9402 (mm) cc_final: 0.9183 (mt) REVERT: E 453 LYS cc_start: 0.9564 (mtpp) cc_final: 0.9270 (mmtt) REVERT: E 456 MET cc_start: 0.8204 (mmp) cc_final: 0.7402 (tpp) outliers start: 1 outliers final: 1 residues processed: 146 average time/residue: 0.1013 time to fit residues: 25.0380 Evaluate side-chains 112 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 61 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 32 optimal weight: 0.0870 chunk 212 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 218 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 chunk 217 optimal weight: 0.0000 chunk 148 optimal weight: 8.9990 overall best weight: 2.1766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN A 683 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.043732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.032256 restraints weight = 142047.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.033253 restraints weight = 86159.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.033913 restraints weight = 61576.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.034411 restraints weight = 49088.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.034712 restraints weight = 41961.644| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18687 Z= 0.129 Angle : 0.583 7.406 25392 Z= 0.285 Chirality : 0.041 0.222 2945 Planarity : 0.005 0.053 3214 Dihedral : 4.524 59.830 2523 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.18), residues: 2287 helix: 1.54 (0.17), residues: 1027 sheet: 0.38 (0.30), residues: 314 loop : -1.05 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 640 TYR 0.015 0.001 TYR B 413 PHE 0.022 0.001 PHE B 544 TRP 0.017 0.001 TRP A 831 HIS 0.004 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00286 (18685) covalent geometry : angle 0.58282 (25386) hydrogen bonds : bond 0.04008 ( 879) hydrogen bonds : angle 4.47662 ( 2541) link_NAG-ASN : bond 0.00185 ( 2) link_NAG-ASN : angle 1.68769 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 289 MET cc_start: 0.7428 (mmp) cc_final: 0.7180 (mmp) REVERT: B 447 GLN cc_start: 0.8618 (mt0) cc_final: 0.8373 (mt0) REVERT: B 617 MET cc_start: 0.9241 (mmp) cc_final: 0.8915 (mmm) REVERT: B 679 PHE cc_start: 0.9033 (t80) cc_final: 0.8787 (t80) REVERT: B 683 GLN cc_start: 0.8472 (mp10) cc_final: 0.8210 (mm-40) REVERT: B 806 PHE cc_start: 0.8583 (t80) cc_final: 0.8338 (t80) REVERT: A 112 ARG cc_start: 0.7762 (tmm160) cc_final: 0.7491 (ttp80) REVERT: A 663 MET cc_start: 0.9244 (tpp) cc_final: 0.9018 (tpp) REVERT: A 664 MET cc_start: 0.8348 (pmm) cc_final: 0.8140 (pmm) REVERT: A 675 PHE cc_start: 0.9017 (t80) cc_final: 0.8670 (t80) REVERT: A 683 GLN cc_start: 0.9278 (mm110) cc_final: 0.8797 (mm110) REVERT: A 769 LEU cc_start: 0.9430 (mm) cc_final: 0.9203 (mt) REVERT: E 453 LYS cc_start: 0.9563 (mtpp) cc_final: 0.9281 (mmtt) REVERT: E 610 LEU cc_start: 0.9176 (tp) cc_final: 0.8773 (tp) REVERT: E 618 MET cc_start: 0.7746 (mmp) cc_final: 0.7534 (mmm) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1035 time to fit residues: 25.4938 Evaluate side-chains 119 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 55 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 216 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 83 optimal weight: 0.0870 chunk 20 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 GLN B 683 GLN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 390 ASN ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.044303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.032754 restraints weight = 143728.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.033774 restraints weight = 86385.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.034455 restraints weight = 61846.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.034928 restraints weight = 49396.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.035217 restraints weight = 42419.340| |-----------------------------------------------------------------------------| r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18687 Z= 0.105 Angle : 0.564 6.961 25392 Z= 0.272 Chirality : 0.040 0.215 2945 Planarity : 0.004 0.050 3214 Dihedral : 4.308 55.988 2523 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.05 % Allowed : 0.85 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 2287 helix: 1.62 (0.17), residues: 1040 sheet: 0.47 (0.30), residues: 314 loop : -0.99 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 730 TYR 0.017 0.001 TYR A 824 PHE 0.020 0.001 PHE B 544 TRP 0.016 0.001 TRP A 831 HIS 0.003 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00232 (18685) covalent geometry : angle 0.56392 (25386) hydrogen bonds : bond 0.03722 ( 879) hydrogen bonds : angle 4.33537 ( 2541) link_NAG-ASN : bond 0.00213 ( 2) link_NAG-ASN : angle 1.50820 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 64 LEU cc_start: 0.8325 (tp) cc_final: 0.8085 (pt) REVERT: B 289 MET cc_start: 0.7421 (mmp) cc_final: 0.7174 (mmp) REVERT: B 447 GLN cc_start: 0.8637 (mt0) cc_final: 0.8248 (mt0) REVERT: B 617 MET cc_start: 0.9235 (mmp) cc_final: 0.8899 (mmm) REVERT: B 675 PHE cc_start: 0.9404 (t80) cc_final: 0.9161 (t80) REVERT: B 806 PHE cc_start: 0.8562 (t80) cc_final: 0.8317 (t80) REVERT: A 112 ARG cc_start: 0.7824 (tmm160) cc_final: 0.7583 (ttp80) REVERT: A 559 MET cc_start: 0.8167 (tpt) cc_final: 0.7785 (tpt) REVERT: A 663 MET cc_start: 0.9247 (tpp) cc_final: 0.9026 (tpp) REVERT: A 675 PHE cc_start: 0.9046 (t80) cc_final: 0.8651 (t80) REVERT: A 683 GLN cc_start: 0.9268 (mm110) cc_final: 0.8836 (mm110) REVERT: A 769 LEU cc_start: 0.9422 (mm) cc_final: 0.9177 (mt) REVERT: E 334 MET cc_start: 0.8580 (ptm) cc_final: 0.8154 (ptm) REVERT: E 453 LYS cc_start: 0.9557 (mtpp) cc_final: 0.9290 (mmtt) REVERT: E 456 MET cc_start: 0.8221 (mmp) cc_final: 0.7437 (tpp) REVERT: E 610 LEU cc_start: 0.9154 (tp) cc_final: 0.8768 (tp) REVERT: E 618 MET cc_start: 0.7811 (mmp) cc_final: 0.7586 (mmm) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.1016 time to fit residues: 26.3794 Evaluate side-chains 119 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 155 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 200 optimal weight: 0.5980 chunk 218 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 ASN ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 ASN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN E 390 ASN ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.043345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.031919 restraints weight = 145759.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.032915 restraints weight = 87536.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.033577 restraints weight = 62547.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.034031 restraints weight = 49973.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.034311 restraints weight = 43042.051| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18687 Z= 0.175 Angle : 0.627 9.987 25392 Z= 0.310 Chirality : 0.042 0.210 2945 Planarity : 0.005 0.049 3214 Dihedral : 4.566 55.206 2523 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.05 % Allowed : 0.50 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.18), residues: 2287 helix: 1.49 (0.17), residues: 1033 sheet: 0.39 (0.30), residues: 314 loop : -1.02 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 730 TYR 0.015 0.002 TYR B 413 PHE 0.042 0.002 PHE B 679 TRP 0.014 0.002 TRP A 105 HIS 0.007 0.001 HIS E 532 Details of bonding type rmsd covalent geometry : bond 0.00385 (18685) covalent geometry : angle 0.62689 (25386) hydrogen bonds : bond 0.04255 ( 879) hydrogen bonds : angle 4.56157 ( 2541) link_NAG-ASN : bond 0.00207 ( 2) link_NAG-ASN : angle 1.72263 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 64 LEU cc_start: 0.8448 (tp) cc_final: 0.8176 (pt) REVERT: B 289 MET cc_start: 0.7445 (mmp) cc_final: 0.7200 (mmp) REVERT: B 392 TYR cc_start: 0.8315 (m-80) cc_final: 0.8074 (m-80) REVERT: B 447 GLN cc_start: 0.8715 (mt0) cc_final: 0.8468 (mt0) REVERT: B 617 MET cc_start: 0.9226 (mmp) cc_final: 0.8911 (mmm) REVERT: B 806 PHE cc_start: 0.8704 (t80) cc_final: 0.8467 (t80) REVERT: A 31 MET cc_start: 0.3030 (tpt) cc_final: 0.2828 (tpt) REVERT: A 112 ARG cc_start: 0.7862 (tmm160) cc_final: 0.7536 (ttp80) REVERT: A 617 MET cc_start: 0.8771 (mmt) cc_final: 0.8297 (mmm) REVERT: A 663 MET cc_start: 0.9226 (tpp) cc_final: 0.9017 (tpp) REVERT: A 859 LEU cc_start: 0.9279 (tt) cc_final: 0.8851 (mt) REVERT: E 334 MET cc_start: 0.8764 (ptm) cc_final: 0.8314 (ptm) REVERT: E 453 LYS cc_start: 0.9562 (mtpp) cc_final: 0.9277 (mmtt) REVERT: E 610 LEU cc_start: 0.9218 (tp) cc_final: 0.8852 (tp) outliers start: 1 outliers final: 1 residues processed: 138 average time/residue: 0.1034 time to fit residues: 24.1497 Evaluate side-chains 113 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 113 optimal weight: 7.9990 chunk 219 optimal weight: 7.9990 chunk 187 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 208 optimal weight: 8.9990 chunk 8 optimal weight: 0.4980 chunk 226 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 390 ASN ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.043458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.031957 restraints weight = 145476.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.032947 restraints weight = 87611.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.033610 restraints weight = 62769.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.034072 restraints weight = 50157.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.034358 restraints weight = 43150.280| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18687 Z= 0.153 Angle : 0.607 8.252 25392 Z= 0.298 Chirality : 0.041 0.216 2945 Planarity : 0.005 0.049 3214 Dihedral : 4.555 54.379 2523 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.05 % Allowed : 0.25 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.18), residues: 2287 helix: 1.45 (0.17), residues: 1040 sheet: 0.37 (0.30), residues: 319 loop : -1.06 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 74 TYR 0.016 0.002 TYR B 413 PHE 0.019 0.001 PHE B 471 TRP 0.015 0.001 TRP A 105 HIS 0.005 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00339 (18685) covalent geometry : angle 0.60656 (25386) hydrogen bonds : bond 0.04143 ( 879) hydrogen bonds : angle 4.54073 ( 2541) link_NAG-ASN : bond 0.00182 ( 2) link_NAG-ASN : angle 1.64269 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 114 PHE cc_start: 0.8973 (t80) cc_final: 0.8574 (t80) REVERT: B 289 MET cc_start: 0.7432 (mmp) cc_final: 0.7196 (mmp) REVERT: B 392 TYR cc_start: 0.8374 (m-80) cc_final: 0.8145 (m-80) REVERT: B 447 GLN cc_start: 0.8677 (mt0) cc_final: 0.8433 (mt0) REVERT: B 617 MET cc_start: 0.9227 (mmp) cc_final: 0.8914 (mmm) REVERT: B 776 MET cc_start: 0.7902 (mtm) cc_final: 0.7693 (mtp) REVERT: B 806 PHE cc_start: 0.8710 (t80) cc_final: 0.8504 (t80) REVERT: A 112 ARG cc_start: 0.7963 (tmm160) cc_final: 0.7611 (ttp80) REVERT: A 617 MET cc_start: 0.8780 (mmt) cc_final: 0.8230 (mmm) REVERT: A 663 MET cc_start: 0.9218 (tpp) cc_final: 0.9005 (tpp) REVERT: A 859 LEU cc_start: 0.9281 (tt) cc_final: 0.8841 (mt) REVERT: E 26 LEU cc_start: 0.9009 (tp) cc_final: 0.8715 (tt) REVERT: E 334 MET cc_start: 0.8748 (ptm) cc_final: 0.8288 (ptm) REVERT: E 453 LYS cc_start: 0.9551 (mtpp) cc_final: 0.9275 (mmtt) REVERT: E 610 LEU cc_start: 0.9209 (tp) cc_final: 0.8834 (tp) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.1040 time to fit residues: 24.1701 Evaluate side-chains 113 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 81 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 ASN B 683 GLN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 ASN A 683 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 532 HIS ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.043920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.032370 restraints weight = 144141.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.033366 restraints weight = 87504.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.034041 restraints weight = 62666.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.034514 restraints weight = 50121.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.034818 restraints weight = 43109.647| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18687 Z= 0.115 Angle : 0.579 8.582 25392 Z= 0.281 Chirality : 0.041 0.217 2945 Planarity : 0.004 0.049 3214 Dihedral : 4.343 51.020 2523 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 2287 helix: 1.57 (0.17), residues: 1046 sheet: 0.46 (0.29), residues: 322 loop : -1.04 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 730 TYR 0.014 0.001 TYR B 413 PHE 0.020 0.001 PHE B 471 TRP 0.017 0.001 TRP A 831 HIS 0.004 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00255 (18685) covalent geometry : angle 0.57875 (25386) hydrogen bonds : bond 0.03900 ( 879) hydrogen bonds : angle 4.38861 ( 2541) link_NAG-ASN : bond 0.00206 ( 2) link_NAG-ASN : angle 1.57566 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2267.21 seconds wall clock time: 41 minutes 14.22 seconds (2474.22 seconds total)