Starting phenix.real_space_refine on Sat Jul 4 04:58:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tw0_26146/07_2026/7tw0_26146.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tw0_26146/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7tw0_26146/07_2026/7tw0_26146.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tw0_26146/07_2026/7tw0_26146.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tw0_26146/07_2026/7tw0_26146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tw0_26146/07_2026/7tw0_26146.map" model { file = "/net/cci-nas-00/data/ceres_data/7tw0_26146/07_2026/7tw0_26146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tw0_26146/07_2026/7tw0_26146.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 chiralities: 1 Time building chain proxies: 2.91, per 1000 atoms: 0.16 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: 0.99 Conformation dependent library (CDL) restraints added in 551.0 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: 0.39 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: 2.74 Time building geometry restraints manager: 1.32 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: 10152 17.95 - 35.89: 861 35.89 - 53.84: 113 53.84 - 71.78: 30 71.78 - 89.73: 20 Dihedral angle restraints: 11176 sinusoidal: 4501 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 11173 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.020 Process input model: 12.480 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 : 13.841 89.727 6852 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/Z covalent geometry : bond 0.00277 / 0.14 (18685) covalent geometry : angle 0.72675 / 0.36 (25386) hydrogen bonds : bond 0.13717 / 9.07 ( 879) hydrogen bonds : angle 5.49419 / 3.76 ( 2541) link_NAG-ASN : bond 0.00223 / 0.11 ( 2) link_NAG-ASN : angle 1.08894 / 0.96 ( 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 : 0.601 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: 0.1040 time to fit residues: 30.3765 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 : 0.598 ------------------------------------------------------------------------------- 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... ** 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 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 = 0.042261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.030709 restraints weight = 148249.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.031653 restraints weight = 89926.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.032307 restraints weight = 64864.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.032745 restraints weight = 52081.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.033041 restraints weight = 45022.120| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 18687 Z= 0.338 Angle : 0.853 12.361 25392 Z= 0.432 Chirality : 0.047 0.224 2945 Planarity : 0.007 0.060 3214 Dihedral : 4.981 23.886 2481 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.40 % Allowed : 7.37 % Favored : 92.23 % 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: -0.22 (0.17), residues: 2287 helix: 0.75 (0.16), residues: 1023 sheet: 0.12 (0.28), residues: 325 loop : -1.20 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 150 TYR 0.024 0.003 TYR B 299 PHE 0.029 0.003 PHE B 591 TRP 0.022 0.003 TRP A 75 HIS 0.014 0.002 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.34 (18685) covalent geometry : angle 0.85266 / 0.43 (25386) hydrogen bonds : bond 0.05848 / 3.83 ( 879) hydrogen bonds : angle 5.33225 / 3.73 ( 2541) link_NAG-ASN : bond 0.00240 / 0.13 ( 2) link_NAG-ASN : angle 2.23918 / 1.93 ( 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 144 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: B 289 MET cc_start: 0.7537 (mmp) cc_final: 0.7309 (mmp) REVERT: B 617 MET cc_start: 0.9242 (mmp) cc_final: 0.8914 (mmm) REVERT: B 683 GLN cc_start: 0.8771 (mp-120) cc_final: 0.8506 (mm-40) REVERT: B 696 MET cc_start: 0.6199 (mmm) cc_final: 0.5865 (tpt) REVERT: B 741 MET cc_start: 0.6372 (ppp) cc_final: 0.6137 (ppp) REVERT: B 776 MET cc_start: 0.7883 (mtm) cc_final: 0.7520 (mtp) REVERT: B 806 PHE cc_start: 0.8853 (t80) cc_final: 0.8641 (t80) REVERT: A 31 MET cc_start: 0.2730 (tpt) cc_final: 0.2440 (tpt) REVERT: A 663 MET cc_start: 0.9382 (tpp) cc_final: 0.9100 (tpp) REVERT: A 683 GLN cc_start: 0.9284 (mm-40) cc_final: 0.8932 (mm110) REVERT: A 752 GLN cc_start: 0.8139 (tm-30) cc_final: 0.7806 (tm-30) REVERT: E 386 PHE cc_start: 0.9295 (t80) cc_final: 0.9011 (t80) REVERT: E 453 LYS cc_start: 0.9557 (mtpp) cc_final: 0.9307 (mmtt) REVERT: E 618 MET cc_start: 0.8125 (mmp) cc_final: 0.7918 (mmm) REVERT: E 648 MET cc_start: 0.6613 (tpt) cc_final: 0.6386 (tpt) outliers start: 8 outliers final: 4 residues processed: 143 average time/residue: 0.1006 time to fit residues: 24.3458 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 : 0.649 ------------------------------------------------------------------------------- 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: 10.0000 chunk 51 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 229 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 171 optimal weight: 0.5980 chunk 37 optimal weight: 9.9990 chunk 224 optimal weight: 0.9980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 GLN ** B 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.044270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.032467 restraints weight = 142805.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.033493 restraints weight = 86062.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.034190 restraints weight = 61666.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.034647 restraints weight = 49349.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.034975 restraints weight = 42588.410| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18687 Z= 0.113 Angle : 0.581 7.721 25392 Z= 0.285 Chirality : 0.041 0.215 2945 Planarity : 0.005 0.052 3214 Dihedral : 4.234 22.786 2481 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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: 1.45 (0.17), residues: 1032 sheet: 0.36 (0.29), residues: 324 loop : -1.07 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.015 0.001 TYR A 824 PHE 0.018 0.001 PHE A 537 TRP 0.016 0.001 TRP A 105 HIS 0.005 0.001 HIS A 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (18685) covalent geometry : angle 0.58075 / 0.28 (25386) hydrogen bonds : bond 0.04387 / 2.90 ( 879) hydrogen bonds : angle 4.58089 / 3.20 ( 2541) link_NAG-ASN : bond 0.00215 / 0.10 ( 2) link_NAG-ASN : angle 1.57408 / 1.30 ( 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 164 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 114 PHE cc_start: 0.8987 (t80) cc_final: 0.8780 (t80) REVERT: B 289 MET cc_start: 0.7471 (mmp) cc_final: 0.7228 (mmp) REVERT: B 617 MET cc_start: 0.9212 (mmp) cc_final: 0.8891 (mmm) REVERT: B 683 GLN cc_start: 0.8605 (mp-120) cc_final: 0.8291 (mm-40) REVERT: B 806 PHE cc_start: 0.8599 (t80) cc_final: 0.8346 (t80) REVERT: B 874 LEU cc_start: 0.9004 (mm) cc_final: 0.8802 (mt) REVERT: A 663 MET cc_start: 0.9356 (tpp) cc_final: 0.9095 (tpp) REVERT: A 675 PHE cc_start: 0.8975 (t80) cc_final: 0.8719 (t80) REVERT: A 769 LEU cc_start: 0.9411 (mm) cc_final: 0.9182 (mt) REVERT: E 453 LYS cc_start: 0.9566 (mtpp) cc_final: 0.9312 (mmtt) REVERT: E 618 MET cc_start: 0.8036 (mmp) cc_final: 0.7775 (mmm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1093 time to fit residues: 29.8403 Evaluate side-chains 117 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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: 0.5980 chunk 164 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 218 optimal weight: 20.0000 chunk 191 optimal weight: 7.9990 chunk 214 optimal weight: 9.9990 chunk 19 optimal weight: 0.1980 chunk 1 optimal weight: 8.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3035 r_free = 0.3035 target = 0.043744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.032083 restraints weight = 144698.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.033084 restraints weight = 87379.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.033766 restraints weight = 62751.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.034213 restraints weight = 50266.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.034527 restraints weight = 43467.634| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2228 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= 0.155 Angle : 0.600 9.458 25392 Z= 0.295 Chirality : 0.041 0.195 2945 Planarity : 0.005 0.051 3214 Dihedral : 4.218 20.367 2481 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.05 % Allowed : 3.16 % Favored : 96.79 % 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: 1.44 (0.17), residues: 1036 sheet: 0.31 (0.29), residues: 329 loop : -1.04 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 112 TYR 0.015 0.002 TYR E 413 PHE 0.026 0.002 PHE B 544 TRP 0.015 0.001 TRP A 105 HIS 0.006 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (18685) covalent geometry : angle 0.59981 / 0.29 (25386) hydrogen bonds : bond 0.04253 / 2.82 ( 879) hydrogen bonds : angle 4.58597 / 3.21 ( 2541) link_NAG-ASN : bond 0.00172 / 0.08 ( 2) link_NAG-ASN : angle 1.73953 / 1.42 ( 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 153 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 PHE cc_start: 0.9010 (t80) cc_final: 0.8808 (t80) REVERT: B 289 MET cc_start: 0.7519 (mmp) cc_final: 0.7292 (mmp) REVERT: B 617 MET cc_start: 0.9227 (mmp) cc_final: 0.8908 (mmm) REVERT: B 683 GLN cc_start: 0.8696 (mp-120) cc_final: 0.8480 (mm-40) REVERT: B 696 MET cc_start: 0.6026 (mmm) cc_final: 0.5754 (tpt) REVERT: B 806 PHE cc_start: 0.8673 (t80) cc_final: 0.8319 (t80) REVERT: B 833 MET cc_start: 0.7743 (mtm) cc_final: 0.7340 (mtm) REVERT: A 31 MET cc_start: 0.3342 (tpt) cc_final: 0.3040 (tpt) REVERT: A 112 ARG cc_start: 0.8092 (ttp80) cc_final: 0.6957 (ttp80) REVERT: A 663 MET cc_start: 0.9337 (tpp) cc_final: 0.9070 (tpp) REVERT: A 675 PHE cc_start: 0.8994 (t80) cc_final: 0.8653 (t80) REVERT: A 807 ASP cc_start: 0.7920 (m-30) cc_final: 0.7701 (t70) REVERT: E 453 LYS cc_start: 0.9567 (mtpp) cc_final: 0.9310 (mmtt) REVERT: E 618 MET cc_start: 0.7960 (mmp) cc_final: 0.7725 (mmm) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.1146 time to fit residues: 29.1390 Evaluate side-chains 112 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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: 10.0000 chunk 15 optimal weight: 0.0270 chunk 173 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 212 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 168 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 overall best weight: 5.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 683 GLN ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 GLN ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.042684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.031238 restraints weight = 146538.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.032196 restraints weight = 88851.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.032840 restraints weight = 64007.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.033280 restraints weight = 51421.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.033564 restraints weight = 44436.143| |-----------------------------------------------------------------------------| r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 18687 Z= 0.266 Angle : 0.729 10.598 25392 Z= 0.367 Chirality : 0.044 0.200 2945 Planarity : 0.006 0.064 3214 Dihedral : 4.861 22.145 2481 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.19 % 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: -0.09 (0.17), residues: 2287 helix: 0.92 (0.16), residues: 1028 sheet: 0.06 (0.28), residues: 325 loop : -1.18 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 730 TYR 0.021 0.002 TYR E 413 PHE 0.029 0.002 PHE B 544 TRP 0.024 0.002 TRP A 831 HIS 0.010 0.002 HIS E 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.27 (18685) covalent geometry : angle 0.72880 / 0.37 (25386) hydrogen bonds : bond 0.05101 / 3.36 ( 879) hydrogen bonds : angle 5.08088 / 3.59 ( 2541) link_NAG-ASN : bond 0.00281 / 0.14 ( 2) link_NAG-ASN : angle 1.94502 / 1.59 ( 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 144 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: B 289 MET cc_start: 0.7462 (mmp) cc_final: 0.7204 (mmp) REVERT: B 392 TYR cc_start: 0.8372 (m-80) cc_final: 0.8020 (m-80) REVERT: B 500 LEU cc_start: 0.9445 (mt) cc_final: 0.9234 (mt) REVERT: B 617 MET cc_start: 0.9203 (mmp) cc_final: 0.8916 (mmm) REVERT: B 679 PHE cc_start: 0.9295 (t80) cc_final: 0.9091 (t80) REVERT: B 683 GLN cc_start: 0.8700 (mp10) cc_final: 0.8447 (mm-40) REVERT: B 696 MET cc_start: 0.6118 (mmm) cc_final: 0.5770 (tpt) REVERT: B 806 PHE cc_start: 0.8852 (t80) cc_final: 0.8552 (t80) REVERT: B 874 LEU cc_start: 0.9028 (mm) cc_final: 0.8810 (mt) REVERT: A 31 MET cc_start: 0.3500 (tpt) cc_final: 0.3096 (tpt) REVERT: A 663 MET cc_start: 0.9339 (tpp) cc_final: 0.9060 (tpp) REVERT: E 453 LYS cc_start: 0.9597 (mtpp) cc_final: 0.9315 (mmtt) REVERT: E 456 MET cc_start: 0.8228 (mmp) cc_final: 0.7320 (tpp) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.1139 time to fit residues: 27.4687 Evaluate side-chains 105 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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: 3.9990 chunk 49 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 156 optimal weight: 0.0770 chunk 223 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.043801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.032189 restraints weight = 142841.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.033177 restraints weight = 87038.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.033860 restraints weight = 62602.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.034313 restraints weight = 49992.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.034547 restraints weight = 43136.063| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18687 Z= 0.128 Angle : 0.598 8.430 25392 Z= 0.294 Chirality : 0.041 0.213 2945 Planarity : 0.005 0.051 3214 Dihedral : 4.367 22.095 2481 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.05 % Allowed : 2.36 % Favored : 97.59 % 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: 0.35 (0.18), residues: 2287 helix: 1.40 (0.17), residues: 1024 sheet: 0.32 (0.30), residues: 317 loop : -1.11 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 112 TYR 0.015 0.001 TYR A 824 PHE 0.019 0.001 PHE B 544 TRP 0.023 0.001 TRP A 831 HIS 0.006 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (18685) covalent geometry : angle 0.59783 / 0.29 (25386) hydrogen bonds : bond 0.04270 / 2.83 ( 879) hydrogen bonds : angle 4.64262 / 3.27 ( 2541) link_NAG-ASN : bond 0.00195 / 0.09 ( 2) link_NAG-ASN : angle 1.72763 / 1.41 ( 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 151 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 289 MET cc_start: 0.7397 (mmp) cc_final: 0.7152 (mmp) REVERT: B 617 MET cc_start: 0.9219 (mmp) cc_final: 0.8887 (mmm) REVERT: B 683 GLN cc_start: 0.8613 (mp10) cc_final: 0.8384 (mm-40) REVERT: B 696 MET cc_start: 0.6131 (mmm) cc_final: 0.5764 (tpt) REVERT: B 776 MET cc_start: 0.7933 (mtm) cc_final: 0.7642 (mtp) REVERT: B 806 PHE cc_start: 0.8789 (t80) cc_final: 0.8509 (t80) REVERT: A 663 MET cc_start: 0.9286 (tpp) cc_final: 0.9017 (tpp) REVERT: A 769 LEU cc_start: 0.9415 (mm) cc_final: 0.9199 (mt) REVERT: E 453 LYS cc_start: 0.9567 (mtpp) cc_final: 0.9278 (mmtt) REVERT: E 456 MET cc_start: 0.8180 (mmp) cc_final: 0.7284 (tpp) REVERT: E 610 LEU cc_start: 0.9080 (tp) cc_final: 0.8832 (tp) outliers start: 1 outliers final: 1 residues processed: 151 average time/residue: 0.1012 time to fit residues: 26.2876 Evaluate side-chains 116 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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: 8.9990 chunk 104 optimal weight: 0.0770 chunk 32 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 218 optimal weight: 0.0980 chunk 227 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 overall best weight: 2.6344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 ASN B 840 GLN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.043575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.032041 restraints weight = 145052.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.033015 restraints weight = 88590.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.033700 restraints weight = 63607.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.034158 restraints weight = 50884.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.034446 restraints weight = 43742.067| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2931 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= 0.148 Angle : 0.605 8.052 25392 Z= 0.298 Chirality : 0.041 0.200 2945 Planarity : 0.005 0.057 3214 Dihedral : 4.326 20.436 2481 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.05 % Allowed : 2.01 % Favored : 97.94 % 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: 0.35 (0.18), residues: 2287 helix: 1.40 (0.17), residues: 1027 sheet: 0.30 (0.30), residues: 308 loop : -1.10 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 50 TYR 0.014 0.001 TYR B 413 PHE 0.022 0.002 PHE B 544 TRP 0.016 0.001 TRP A 831 HIS 0.005 0.001 HIS A 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (18685) covalent geometry : angle 0.60447 / 0.30 (25386) hydrogen bonds : bond 0.04246 / 2.81 ( 879) hydrogen bonds : angle 4.63395 / 3.27 ( 2541) link_NAG-ASN : bond 0.00197 / 0.09 ( 2) link_NAG-ASN : angle 1.73597 / 1.39 ( 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 145 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 LEU cc_start: 0.8413 (tp) cc_final: 0.8036 (pt) REVERT: B 289 MET cc_start: 0.7425 (mmp) cc_final: 0.7179 (mmp) REVERT: B 617 MET cc_start: 0.9232 (mmp) cc_final: 0.8904 (mmm) REVERT: B 683 GLN cc_start: 0.8526 (mp10) cc_final: 0.8256 (mm-40) REVERT: B 806 PHE cc_start: 0.8763 (t80) cc_final: 0.8515 (t80) REVERT: A 617 MET cc_start: 0.8764 (mmt) cc_final: 0.8303 (mmm) REVERT: A 663 MET cc_start: 0.9207 (tpp) cc_final: 0.8984 (tpp) REVERT: A 664 MET cc_start: 0.8388 (pmm) cc_final: 0.8176 (pmm) REVERT: A 675 PHE cc_start: 0.9032 (t80) cc_final: 0.8721 (t80) REVERT: A 769 LEU cc_start: 0.9426 (mm) cc_final: 0.9199 (mt) REVERT: E 453 LYS cc_start: 0.9575 (mtpp) cc_final: 0.9320 (mmtt) REVERT: E 456 MET cc_start: 0.8168 (mmp) cc_final: 0.7278 (tpp) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.1051 time to fit residues: 26.0384 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 : 0.595 ------------------------------------------------------------------------------- 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: 4.9990 chunk 27 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 201 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 11 optimal weight: 0.0270 overall best weight: 2.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.043640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.032224 restraints weight = 142379.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.033215 restraints weight = 86669.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.033896 restraints weight = 62129.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.034372 restraints weight = 49389.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.034698 restraints weight = 42272.068| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18687 Z= 0.133 Angle : 0.588 7.621 25392 Z= 0.288 Chirality : 0.041 0.199 2945 Planarity : 0.005 0.049 3214 Dihedral : 4.228 21.090 2481 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.05 % Allowed : 1.10 % Favored : 98.85 % 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: 1.50 (0.17), residues: 1027 sheet: 0.37 (0.30), residues: 322 loop : -1.11 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 730 TYR 0.015 0.001 TYR A 824 PHE 0.021 0.001 PHE B 544 TRP 0.016 0.001 TRP A 105 HIS 0.005 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (18685) covalent geometry : angle 0.58795 / 0.29 (25386) hydrogen bonds : bond 0.04086 / 2.71 ( 879) hydrogen bonds : angle 4.53349 / 3.19 ( 2541) link_NAG-ASN : bond 0.00177 / 0.08 ( 2) link_NAG-ASN : angle 1.62484 / 1.31 ( 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 147 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 LEU cc_start: 0.8430 (tp) cc_final: 0.8110 (pt) REVERT: B 289 MET cc_start: 0.7424 (mmp) cc_final: 0.7181 (mmp) REVERT: B 617 MET cc_start: 0.9241 (mmp) cc_final: 0.8914 (mmm) REVERT: B 683 GLN cc_start: 0.8539 (mp10) cc_final: 0.8268 (mm-40) REVERT: B 806 PHE cc_start: 0.8681 (t80) cc_final: 0.8445 (t80) REVERT: A 617 MET cc_start: 0.8757 (mmt) cc_final: 0.8272 (mmm) REVERT: A 663 MET cc_start: 0.9236 (tpp) cc_final: 0.9007 (tpp) REVERT: A 675 PHE cc_start: 0.9076 (t80) cc_final: 0.8769 (t80) REVERT: A 769 LEU cc_start: 0.9433 (mm) cc_final: 0.9199 (mt) REVERT: A 859 LEU cc_start: 0.9281 (tt) cc_final: 0.8850 (mt) REVERT: E 453 LYS cc_start: 0.9567 (mtpp) cc_final: 0.9303 (mmtt) REVERT: E 610 LEU cc_start: 0.9162 (tp) cc_final: 0.8806 (tp) outliers start: 1 outliers final: 1 residues processed: 147 average time/residue: 0.0972 time to fit residues: 24.5464 Evaluate side-chains 117 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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: 9.9990 chunk 200 optimal weight: 5.9990 chunk 218 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 172 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 204 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 GLN ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** 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 532 HIS ** 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 = 0.3011 r_free = 0.3011 target = 0.043031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.031647 restraints weight = 145884.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.032630 restraints weight = 88726.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.033289 restraints weight = 63512.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.033729 restraints weight = 50757.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.034037 restraints weight = 43789.576| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 18687 Z= 0.212 Angle : 0.680 9.253 25392 Z= 0.338 Chirality : 0.043 0.205 2945 Planarity : 0.005 0.049 3214 Dihedral : 4.605 20.445 2481 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.05 % Allowed : 0.55 % Favored : 99.40 % 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: 0.09 (0.17), residues: 2287 helix: 1.11 (0.16), residues: 1039 sheet: 0.14 (0.29), residues: 321 loop : -1.17 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 283 TYR 0.017 0.002 TYR E 413 PHE 0.025 0.002 PHE B 544 TRP 0.015 0.002 TRP A 105 HIS 0.007 0.001 HIS E 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (18685) covalent geometry : angle 0.67951 / 0.34 (25386) hydrogen bonds : bond 0.04656 / 3.09 ( 879) hydrogen bonds : angle 4.87497 / 3.44 ( 2541) link_NAG-ASN : bond 0.00257 / 0.13 ( 2) link_NAG-ASN : angle 1.89470 / 1.52 ( 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 : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 LEU cc_start: 0.8457 (tp) cc_final: 0.8159 (pt) REVERT: B 114 PHE cc_start: 0.9005 (t80) cc_final: 0.8683 (t80) REVERT: B 289 MET cc_start: 0.7426 (mmp) cc_final: 0.7161 (mmp) REVERT: B 392 TYR cc_start: 0.8374 (m-80) cc_final: 0.8087 (m-80) REVERT: B 617 MET cc_start: 0.9218 (mmp) cc_final: 0.8918 (mmm) REVERT: B 683 GLN cc_start: 0.8546 (mp10) cc_final: 0.8307 (mm-40) REVERT: B 806 PHE cc_start: 0.8820 (t80) cc_final: 0.8614 (t80) REVERT: A 31 MET cc_start: 0.3405 (tpt) cc_final: 0.3202 (tpt) REVERT: A 76 MET cc_start: 0.8475 (tpt) cc_final: 0.8184 (tpt) REVERT: A 617 MET cc_start: 0.8821 (mmt) cc_final: 0.8356 (mmm) REVERT: A 663 MET cc_start: 0.9205 (tpp) cc_final: 0.8994 (tpp) REVERT: A 683 GLN cc_start: 0.9276 (mm110) cc_final: 0.8867 (mm110) REVERT: E 57 LYS cc_start: 0.8760 (ttmt) cc_final: 0.8440 (tptp) REVERT: E 453 LYS cc_start: 0.9619 (mtpp) cc_final: 0.9335 (mmtt) REVERT: E 456 MET cc_start: 0.8187 (mmp) cc_final: 0.7262 (tpp) REVERT: E 610 LEU cc_start: 0.9183 (tp) cc_final: 0.8701 (tp) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.0976 time to fit residues: 23.0584 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 : 0.566 ------------------------------------------------------------------------------- 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: 0.9990 chunk 219 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 205 optimal weight: 1.9990 chunk 208 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 226 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 GLN B 840 GLN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3025 r_free = 0.3025 target = 0.043501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.032040 restraints weight = 145721.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.033028 restraints weight = 87632.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.033707 restraints weight = 62793.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.034164 restraints weight = 50233.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.034452 restraints weight = 43120.550| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18687 Z= 0.150 Angle : 0.616 8.219 25392 Z= 0.304 Chirality : 0.042 0.211 2945 Planarity : 0.005 0.049 3214 Dihedral : 4.424 22.135 2481 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % 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: 0.24 (0.18), residues: 2287 helix: 1.26 (0.17), residues: 1040 sheet: 0.32 (0.30), residues: 320 loop : -1.17 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 74 TYR 0.016 0.002 TYR A 824 PHE 0.022 0.001 PHE B 544 TRP 0.016 0.001 TRP A 105 HIS 0.006 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (18685) covalent geometry : angle 0.61571 / 0.30 (25386) hydrogen bonds : bond 0.04287 / 2.85 ( 879) hydrogen bonds : angle 4.72241 / 3.33 ( 2541) link_NAG-ASN : bond 0.00190 / 0.09 ( 2) link_NAG-ASN : angle 1.74230 / 1.41 ( 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 139 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 64 LEU cc_start: 0.8438 (tp) cc_final: 0.8144 (pt) REVERT: B 114 PHE cc_start: 0.8997 (t80) cc_final: 0.8552 (t80) REVERT: B 289 MET cc_start: 0.7433 (mmp) cc_final: 0.7189 (mmp) REVERT: B 392 TYR cc_start: 0.8381 (m-80) cc_final: 0.8111 (m-80) REVERT: B 617 MET cc_start: 0.9225 (mmp) cc_final: 0.8917 (mmm) REVERT: B 683 GLN cc_start: 0.8454 (mp10) cc_final: 0.8216 (mm-40) REVERT: A 471 PHE cc_start: 0.9524 (t80) cc_final: 0.9260 (t80) REVERT: A 559 MET cc_start: 0.8404 (tpt) cc_final: 0.8058 (tpt) REVERT: A 617 MET cc_start: 0.8762 (mmt) cc_final: 0.8282 (mmm) REVERT: A 663 MET cc_start: 0.9195 (tpp) cc_final: 0.8965 (tpp) REVERT: A 664 MET cc_start: 0.8263 (pmm) cc_final: 0.8052 (pmm) REVERT: A 675 PHE cc_start: 0.9056 (t80) cc_final: 0.8669 (t80) REVERT: A 859 LEU cc_start: 0.9299 (tt) cc_final: 0.8843 (mt) REVERT: E 26 LEU cc_start: 0.9005 (tp) cc_final: 0.8714 (tt) REVERT: E 57 LYS cc_start: 0.8812 (ttmt) cc_final: 0.8474 (tptp) REVERT: E 453 LYS cc_start: 0.9590 (mtpp) cc_final: 0.9310 (mmtt) REVERT: E 610 LEU cc_start: 0.9157 (tp) cc_final: 0.8804 (tp) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1128 time to fit residues: 26.6479 Evaluate side-chains 111 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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: 10.0000 chunk 169 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 146 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 54 optimal weight: 0.3980 chunk 160 optimal weight: 0.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 GLN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.043951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.032431 restraints weight = 144898.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.033427 restraints weight = 87944.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.034111 restraints weight = 63132.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.034574 restraints weight = 50438.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.034890 restraints weight = 43419.500| |-----------------------------------------------------------------------------| r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18687 Z= 0.120 Angle : 0.595 10.816 25392 Z= 0.289 Chirality : 0.041 0.213 2945 Planarity : 0.005 0.049 3214 Dihedral : 4.199 20.249 2481 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.05 % Allowed : 0.45 % Favored : 99.50 % 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: 1.46 (0.17), residues: 1033 sheet: 0.44 (0.30), residues: 320 loop : -1.09 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 50 TYR 0.014 0.001 TYR B 413 PHE 0.023 0.001 PHE B 806 TRP 0.017 0.001 TRP A 105 HIS 0.005 0.001 HIS A 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (18685) covalent geometry : angle 0.59481 / 0.29 (25386) hydrogen bonds : bond 0.03988 / 2.64 ( 879) hydrogen bonds : angle 4.56026 / 3.21 ( 2541) link_NAG-ASN : bond 0.00201 / 0.10 ( 2) link_NAG-ASN : angle 1.69405 / 1.35 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2332.71 seconds wall clock time: 41 minutes 26.55 seconds (2486.55 seconds total)