Starting phenix.real_space_refine on Mon Jun 16 10:03:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tw0_26146/06_2025/7tw0_26146.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tw0_26146/06_2025/7tw0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tw0_26146/06_2025/7tw0_26146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tw0_26146/06_2025/7tw0_26146.map" model { file = "/net/cci-nas-00/data/ceres_data/7tw0_26146/06_2025/7tw0_26146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tw0_26146/06_2025/7tw0_26146.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18266 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 6435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6435 Classifications: {'peptide': 814} Link IDs: {'PTRANS': 49, 'TRANS': 764} Chain breaks: 3 Chain: "A" Number of atoms: 6563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6563 Classifications: {'peptide': 830} Link IDs: {'PTRANS': 49, 'TRANS': 780} Chain breaks: 3 Chain: "E" Number of atoms: 5240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5240 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 31, 'TRANS': 633} Chain breaks: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.44, per 1000 atoms: 0.57 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: 4.36 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.23 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: 6.77 Time building geometry restraints manager: 5.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5056 1.33 - 1.45: 3169 1.45 - 1.57: 10341 1.57 - 1.69: 0 1.69 - 1.81: 119 Bond restraints: 18685 Sorted by residual: bond pdb=" N LEU A 775 " pdb=" CA LEU A 775 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.10e-02 8.26e+03 6.62e+00 bond pdb=" C PRO A 563 " pdb=" O PRO A 563 " ideal model delta sigma weight residual 1.235 1.217 0.018 1.30e-02 5.92e+03 1.94e+00 bond pdb=" C1 NAG B1000 " pdb=" O5 NAG B1000 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.87e+00 bond pdb=" C1 NAG A1000 " pdb=" O5 NAG A1000 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.81e+00 bond pdb=" CG LEU B 540 " pdb=" CD2 LEU B 540 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.76e+00 ... (remaining 18680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 24803 2.01 - 4.02: 463 4.02 - 6.03: 82 6.03 - 8.04: 26 8.04 - 10.05: 12 Bond angle restraints: 25386 Sorted by residual: angle pdb=" N GLU B 218 " pdb=" CA GLU B 218 " pdb=" CB GLU B 218 " ideal model delta sigma weight residual 110.30 115.97 -5.67 1.54e+00 4.22e-01 1.36e+01 angle pdb=" C VAL A 446 " pdb=" N GLN A 447 " pdb=" CA GLN A 447 " ideal model delta sigma weight residual 120.72 114.95 5.77 1.67e+00 3.59e-01 1.20e+01 angle pdb=" C LEU B 217 " pdb=" N GLU B 218 " pdb=" CA GLU B 218 " ideal model delta sigma weight residual 120.68 114.86 5.82 1.70e+00 3.46e-01 1.17e+01 angle pdb=" N PHE B 597 " pdb=" CA PHE B 597 " pdb=" C PHE B 597 " ideal model delta sigma weight residual 108.07 110.99 -2.92 8.90e-01 1.26e+00 1.08e+01 angle pdb=" CB MET B 712 " pdb=" CG MET B 712 " pdb=" SD MET B 712 " ideal model delta sigma weight residual 112.70 122.32 -9.62 3.00e+00 1.11e-01 1.03e+01 ... (remaining 25381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10188 17.95 - 35.89: 865 35.89 - 53.84: 115 53.84 - 71.78: 30 71.78 - 89.73: 20 Dihedral angle restraints: 11218 sinusoidal: 4543 harmonic: 6675 Sorted by residual: dihedral pdb=" CA PRO A 568 " pdb=" C PRO A 568 " pdb=" N ASN A 569 " pdb=" CA ASN A 569 " ideal model delta harmonic sigma weight residual -180.00 -161.03 -18.97 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA TRP B 81 " pdb=" C TRP B 81 " pdb=" N VAL B 82 " pdb=" CA VAL B 82 " ideal model delta harmonic sigma weight residual 180.00 163.10 16.90 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA GLN E 225 " pdb=" C GLN E 225 " pdb=" N ARG E 226 " pdb=" CA ARG E 226 " ideal model delta harmonic sigma weight residual -180.00 -163.20 -16.80 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 11215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2440 0.058 - 0.116: 446 0.116 - 0.174: 53 0.174 - 0.232: 4 0.232 - 0.290: 2 Chirality restraints: 2945 Sorted by residual: chirality pdb=" CB ILE E 81 " pdb=" CA ILE E 81 " pdb=" CG1 ILE E 81 " pdb=" CG2 ILE E 81 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB ILE B 783 " pdb=" CA ILE B 783 " pdb=" CG1 ILE B 783 " pdb=" CG2 ILE B 783 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA GLN A 447 " pdb=" N GLN A 447 " pdb=" C GLN A 447 " pdb=" CB GLN A 447 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.07e-01 ... (remaining 2942 not shown) Planarity restraints: 3216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 634 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.12e+00 pdb=" N PRO B 635 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 635 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 635 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 390 " -0.038 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO A 391 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 391 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 391 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 544 " -0.019 2.00e-02 2.50e+03 1.70e-02 5.03e+00 pdb=" CG PHE B 544 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE B 544 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 544 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 544 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 544 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE B 544 " -0.000 2.00e-02 2.50e+03 ... (remaining 3213 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 567 2.72 - 3.26: 17894 3.26 - 3.81: 28591 3.81 - 4.35: 33633 4.35 - 4.90: 58320 Nonbonded interactions: 139005 Sorted by model distance: nonbonded pdb=" O LEU B 863 " pdb=" OG1 THR B 866 " model vdw 2.169 3.040 nonbonded pdb=" O PHE B 679 " pdb=" NE2 GLN B 683 " model vdw 2.186 3.120 nonbonded pdb=" OD2 ASP E 199 " pdb=" NE2 HIS E 210 " model vdw 2.275 3.120 nonbonded pdb=" OD1 ASP B 137 " pdb=" NH1 ARG B 150 " model vdw 2.280 3.120 nonbonded pdb=" O THR A 103 " pdb=" OG SER A 106 " model vdw 2.286 3.040 ... (remaining 139000 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 55 through 894 or resid 1000)) selection = (chain 'B' and (resid 55 through 348 or resid 369 through 894 or resid 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: 1.910 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: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 42.080 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18687 Z= 0.141 Angle : 0.727 10.055 25392 Z= 0.365 Chirality : 0.044 0.290 2945 Planarity : 0.005 0.057 3214 Dihedral : 13.827 89.727 6894 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.05 % Allowed : 0.25 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (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 TRP 0.014 0.001 TRP A 831 HIS 0.008 0.001 HIS B 834 PHE 0.038 0.001 PHE B 544 TYR 0.026 0.001 TYR B 413 ARG 0.004 0.000 ARG B 80 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 2) link_NAG-ASN : angle 1.08894 ( 6) hydrogen bonds : bond 0.13717 ( 879) hydrogen bonds : angle 5.49419 ( 2541) covalent geometry : bond 0.00277 (18685) covalent geometry : angle 0.72675 (25386) *********************** 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 : 2.675 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: 0.8842 (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: 0.8797 (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: 0.8277 (t80) REVERT: B 833 MET cc_start: 0.7424 (mtm) cc_final: 0.7191 (mtm) REVERT: B 874 LEU cc_start: 0.9134 (mm) cc_final: 0.8880 (mt) REVERT: A 31 MET cc_start: 0.2357 (tpt) cc_final: 0.2129 (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: 0.7079 (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: 0.7813 (mmm) REVERT: E 672 MET cc_start: 0.8525 (mmp) cc_final: 0.8319 (mmm) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.2834 time to fit residues: 81.7546 Evaluate side-chains 128 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 10.0000 chunk 174 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 180 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 109 optimal weight: 0.0870 chunk 134 optimal weight: 9.9990 chunk 208 optimal weight: 0.9990 overall best weight: 3.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 517 HIS ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.043737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.032072 restraints weight = 143646.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.033090 restraints weight = 86991.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.033781 restraints weight = 62306.084| |-----------------------------------------------------------------------------| r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18687 Z= 0.163 Angle : 0.602 8.167 25392 Z= 0.300 Chirality : 0.041 0.179 2945 Planarity : 0.005 0.052 3214 Dihedral : 4.196 49.804 2523 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.05 % Allowed : 4.66 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.17), residues: 2287 helix: 1.52 (0.17), residues: 1030 sheet: 0.42 (0.28), residues: 332 loop : -0.97 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 831 HIS 0.007 0.001 HIS E 210 PHE 0.017 0.001 PHE B 294 TYR 0.012 0.001 TYR A 553 ARG 0.005 0.000 ARG A 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 2) link_NAG-ASN : angle 1.29986 ( 6) hydrogen bonds : bond 0.04582 ( 879) hydrogen bonds : angle 4.64039 ( 2541) covalent geometry : bond 0.00358 (18685) covalent geometry : angle 0.60183 (25386) *********************** 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 151 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 4.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 PHE cc_start: 0.9066 (t80) cc_final: 0.8795 (t80) REVERT: B 289 MET cc_start: 0.7590 (mmp) cc_final: 0.7352 (mmp) REVERT: B 578 MET cc_start: 0.8385 (ttp) cc_final: 0.8162 (tmm) REVERT: B 617 MET cc_start: 0.9274 (mmp) cc_final: 0.8948 (mmm) REVERT: B 776 MET cc_start: 0.7761 (mtm) cc_final: 0.7489 (mtp) REVERT: B 806 PHE cc_start: 0.8582 (t80) cc_final: 0.8318 (t80) REVERT: B 874 LEU cc_start: 0.9062 (mm) cc_final: 0.8830 (mt) REVERT: A 31 MET cc_start: 0.2453 (tpt) cc_final: 0.2166 (tpt) REVERT: A 435 MET cc_start: 0.7805 (ptp) cc_final: 0.7157 (pmm) REVERT: A 663 MET cc_start: 0.9401 (tpp) cc_final: 0.9127 (tpp) REVERT: A 683 GLN cc_start: 0.9318 (mm-40) cc_final: 0.8880 (mm110) REVERT: E 386 PHE cc_start: 0.9307 (t80) cc_final: 0.9037 (t80) REVERT: E 618 MET cc_start: 0.8256 (mmp) cc_final: 0.7920 (mmm) REVERT: E 648 MET cc_start: 0.6483 (tpt) cc_final: 0.6025 (tpt) outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.3308 time to fit residues: 87.2794 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 : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 49 optimal weight: 7.9990 chunk 29 optimal weight: 0.0060 chunk 83 optimal weight: 8.9990 chunk 185 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 195 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 overall best weight: 5.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** B 275 HIS ** 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 87 ASN ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 HIS A 330 GLN A 457 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.042467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.030960 restraints weight = 146217.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.031917 restraints weight = 88390.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.032572 restraints weight = 63613.198| |-----------------------------------------------------------------------------| r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 18687 Z= 0.292 Angle : 0.773 10.638 25392 Z= 0.389 Chirality : 0.045 0.250 2945 Planarity : 0.006 0.054 3214 Dihedral : 5.224 57.207 2523 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.20 % Allowed : 6.72 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2287 helix: 0.91 (0.16), residues: 1026 sheet: 0.21 (0.28), residues: 324 loop : -1.15 (0.18), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 831 HIS 0.012 0.002 HIS A 101 PHE 0.045 0.003 PHE A 537 TYR 0.024 0.002 TYR B 299 ARG 0.008 0.001 ARG B 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 2) link_NAG-ASN : angle 2.25425 ( 6) hydrogen bonds : bond 0.05319 ( 879) hydrogen bonds : angle 5.14975 ( 2541) covalent geometry : bond 0.00633 (18685) covalent geometry : angle 0.77225 (25386) *********************** 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 143 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 114 PHE cc_start: 0.9011 (t80) cc_final: 0.8801 (t80) REVERT: B 289 MET cc_start: 0.7585 (mmp) cc_final: 0.7300 (mmp) REVERT: B 435 MET cc_start: 0.7833 (tpt) cc_final: 0.7588 (tpp) REVERT: B 500 LEU cc_start: 0.9438 (mt) cc_final: 0.9225 (mt) REVERT: B 617 MET cc_start: 0.9253 (mmp) cc_final: 0.8963 (mmm) REVERT: B 696 MET cc_start: 0.6165 (mmm) cc_final: 0.5925 (tpt) REVERT: B 776 MET cc_start: 0.7743 (mtm) cc_final: 0.7481 (mtp) REVERT: B 806 PHE cc_start: 0.8780 (t80) cc_final: 0.8568 (t80) REVERT: B 833 MET cc_start: 0.7776 (mtm) cc_final: 0.7428 (mtm) REVERT: A 31 MET cc_start: 0.2501 (tpt) cc_final: 0.2283 (tpt) REVERT: A 663 MET cc_start: 0.9393 (tpp) cc_final: 0.9120 (tpp) REVERT: E 334 MET cc_start: 0.8885 (ptm) cc_final: 0.8667 (ppp) REVERT: E 453 LYS cc_start: 0.9556 (mtpp) cc_final: 0.9318 (mmtt) REVERT: E 618 MET cc_start: 0.8187 (mmp) cc_final: 0.7975 (mmm) outliers start: 4 outliers final: 1 residues processed: 143 average time/residue: 0.3505 time to fit residues: 82.0651 Evaluate side-chains 95 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 96 optimal weight: 0.4980 chunk 84 optimal weight: 7.9990 chunk 19 optimal weight: 0.0270 chunk 229 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 64 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 220 optimal weight: 6.9990 overall best weight: 2.7044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.043703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.032037 restraints weight = 144023.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.033037 restraints weight = 87337.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.033709 restraints weight = 62806.742| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2291 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= 0.149 Angle : 0.602 7.759 25392 Z= 0.300 Chirality : 0.041 0.234 2945 Planarity : 0.005 0.055 3214 Dihedral : 4.733 57.407 2523 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.05 % Allowed : 3.36 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2287 helix: 1.31 (0.17), residues: 1031 sheet: 0.25 (0.29), residues: 327 loop : -1.13 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 105 HIS 0.005 0.001 HIS E 210 PHE 0.013 0.001 PHE E 386 TYR 0.015 0.001 TYR E 413 ARG 0.003 0.000 ARG B 832 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 2) link_NAG-ASN : angle 1.81003 ( 6) hydrogen bonds : bond 0.04439 ( 879) hydrogen bonds : angle 4.71123 ( 2541) covalent geometry : bond 0.00326 (18685) covalent geometry : angle 0.60139 (25386) *********************** 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 154 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 PHE cc_start: 0.9050 (t80) cc_final: 0.8817 (t80) REVERT: B 289 MET cc_start: 0.7404 (mmp) cc_final: 0.7126 (mmp) REVERT: B 500 LEU cc_start: 0.9437 (mt) cc_final: 0.9229 (mt) REVERT: B 617 MET cc_start: 0.9247 (mmp) cc_final: 0.8921 (mmm) REVERT: B 683 GLN cc_start: 0.8719 (mp-120) cc_final: 0.8470 (mm-40) REVERT: B 776 MET cc_start: 0.7903 (mtm) cc_final: 0.7542 (mtt) REVERT: B 806 PHE cc_start: 0.8707 (t80) cc_final: 0.8412 (t80) REVERT: B 833 MET cc_start: 0.7777 (mtm) cc_final: 0.7457 (mtm) REVERT: A 559 MET cc_start: 0.8643 (tpp) cc_final: 0.8357 (tpt) REVERT: A 663 MET cc_start: 0.9371 (tpp) cc_final: 0.9082 (tpp) REVERT: E 453 LYS cc_start: 0.9573 (mtpp) cc_final: 0.9327 (mmtt) REVERT: E 618 MET cc_start: 0.7996 (mmp) cc_final: 0.7780 (mmm) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.4233 time to fit residues: 109.7444 Evaluate side-chains 109 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 3.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 104 optimal weight: 0.0030 chunk 43 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 188 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 683 GLN ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 390 ASN ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 559 ASN ** 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 = 0.3060 r_free = 0.3060 target = 0.044608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.032821 restraints weight = 141109.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.033861 restraints weight = 85526.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.034561 restraints weight = 61140.514| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18687 Z= 0.100 Angle : 0.559 7.116 25392 Z= 0.270 Chirality : 0.040 0.223 2945 Planarity : 0.004 0.050 3214 Dihedral : 4.326 59.610 2523 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2287 helix: 1.66 (0.17), residues: 1039 sheet: 0.48 (0.29), residues: 328 loop : -1.04 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 105 HIS 0.003 0.001 HIS E 210 PHE 0.022 0.001 PHE B 544 TYR 0.015 0.001 TYR A 824 ARG 0.006 0.000 ARG A 730 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 2) link_NAG-ASN : angle 1.50967 ( 6) hydrogen bonds : bond 0.03765 ( 879) hydrogen bonds : angle 4.30617 ( 2541) covalent geometry : bond 0.00210 (18685) covalent geometry : angle 0.55885 (25386) *********************** 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 154 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 PHE cc_start: 0.9045 (t80) cc_final: 0.8835 (t80) REVERT: B 289 MET cc_start: 0.7419 (mmp) cc_final: 0.7155 (mmp) REVERT: B 500 LEU cc_start: 0.9460 (mt) cc_final: 0.9255 (mt) REVERT: B 617 MET cc_start: 0.9281 (mmp) cc_final: 0.8919 (mmm) REVERT: B 679 PHE cc_start: 0.9227 (t80) cc_final: 0.8947 (t80) REVERT: B 683 GLN cc_start: 0.8622 (mp10) cc_final: 0.8303 (mm-40) REVERT: B 776 MET cc_start: 0.8020 (mtm) cc_final: 0.7661 (mtt) REVERT: B 806 PHE cc_start: 0.8570 (t80) cc_final: 0.8316 (t80) REVERT: B 833 MET cc_start: 0.7502 (mtm) cc_final: 0.7277 (mtt) REVERT: A 288 LEU cc_start: 0.9164 (mt) cc_final: 0.8908 (mt) REVERT: A 663 MET cc_start: 0.9305 (tpp) cc_final: 0.9035 (tpp) REVERT: A 675 PHE cc_start: 0.8958 (t80) cc_final: 0.8662 (t80) REVERT: A 683 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8751 (mm110) REVERT: A 769 LEU cc_start: 0.9408 (mm) cc_final: 0.9182 (mt) REVERT: A 807 ASP cc_start: 0.7954 (m-30) cc_final: 0.7745 (t70) REVERT: A 859 LEU cc_start: 0.9214 (tt) cc_final: 0.8804 (mm) REVERT: E 334 MET cc_start: 0.8506 (ptm) cc_final: 0.8102 (ptm) REVERT: E 453 LYS cc_start: 0.9560 (mtpp) cc_final: 0.9287 (mmtt) REVERT: E 456 MET cc_start: 0.8256 (mmp) cc_final: 0.7636 (tpt) REVERT: E 618 MET cc_start: 0.7839 (mmp) cc_final: 0.7616 (mmm) outliers start: 1 outliers final: 1 residues processed: 154 average time/residue: 0.2480 time to fit residues: 64.6691 Evaluate side-chains 126 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 62 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 211 optimal weight: 30.0000 chunk 187 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN A 457 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 559 ASN ** 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 = 0.3008 r_free = 0.3008 target = 0.042885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.031384 restraints weight = 147963.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.032349 restraints weight = 89752.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.033003 restraints weight = 64783.601| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2866 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= 0.256 Angle : 0.717 9.993 25392 Z= 0.358 Chirality : 0.044 0.217 2945 Planarity : 0.006 0.060 3214 Dihedral : 4.985 57.208 2523 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.10 % Allowed : 2.56 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.17), residues: 2287 helix: 1.14 (0.16), residues: 1027 sheet: 0.22 (0.29), residues: 325 loop : -1.11 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 831 HIS 0.008 0.002 HIS E 589 PHE 0.025 0.002 PHE B 544 TYR 0.018 0.002 TYR E 413 ARG 0.005 0.001 ARG A 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 2) link_NAG-ASN : angle 1.92359 ( 6) hydrogen bonds : bond 0.04777 ( 879) hydrogen bonds : angle 4.90707 ( 2541) covalent geometry : bond 0.00559 (18685) covalent geometry : angle 0.71667 (25386) *********************** 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 140 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 PHE cc_start: 0.9056 (t80) cc_final: 0.8800 (t80) REVERT: B 392 TYR cc_start: 0.8270 (m-80) cc_final: 0.7909 (m-80) REVERT: B 500 LEU cc_start: 0.9421 (mt) cc_final: 0.9206 (mt) REVERT: B 617 MET cc_start: 0.9298 (mmp) cc_final: 0.8961 (mmm) REVERT: B 683 GLN cc_start: 0.8625 (mp10) cc_final: 0.8337 (mm-40) REVERT: B 696 MET cc_start: 0.6337 (mmm) cc_final: 0.6114 (tpt) REVERT: B 776 MET cc_start: 0.7865 (mtm) cc_final: 0.7481 (mtt) REVERT: B 806 PHE cc_start: 0.8798 (t80) cc_final: 0.8540 (t80) REVERT: A 31 MET cc_start: 0.3408 (tpt) cc_final: 0.3134 (tpt) REVERT: A 288 LEU cc_start: 0.9172 (mt) cc_final: 0.8919 (mt) REVERT: A 663 MET cc_start: 0.9353 (tpp) cc_final: 0.9101 (tpp) REVERT: A 683 GLN cc_start: 0.9306 (mm-40) cc_final: 0.8881 (mm110) REVERT: E 453 LYS cc_start: 0.9568 (mtpp) cc_final: 0.9302 (mmtt) REVERT: E 456 MET cc_start: 0.8219 (mmp) cc_final: 0.7392 (tpp) REVERT: E 618 MET cc_start: 0.8008 (mmp) cc_final: 0.7772 (mmm) outliers start: 2 outliers final: 0 residues processed: 139 average time/residue: 0.2368 time to fit residues: 55.8692 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 : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 91 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 181 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 chunk 209 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.043803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.032195 restraints weight = 142551.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.033190 restraints weight = 87181.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.033864 restraints weight = 62726.559| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18687 Z= 0.122 Angle : 0.591 7.244 25392 Z= 0.289 Chirality : 0.041 0.233 2945 Planarity : 0.005 0.048 3214 Dihedral : 4.607 59.719 2523 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.05 % Allowed : 1.35 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 2287 helix: 1.45 (0.17), residues: 1027 sheet: 0.40 (0.30), residues: 317 loop : -1.04 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 831 HIS 0.007 0.001 HIS B 161 PHE 0.022 0.001 PHE B 544 TYR 0.015 0.001 TYR B 413 ARG 0.004 0.000 ARG A 730 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 2) link_NAG-ASN : angle 1.78403 ( 6) hydrogen bonds : bond 0.04111 ( 879) hydrogen bonds : angle 4.52628 ( 2541) covalent geometry : bond 0.00268 (18685) covalent geometry : angle 0.59090 (25386) *********************** 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 144 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 2.301 Fit side-chains revert: symmetry clash REVERT: B 64 LEU cc_start: 0.8401 (tp) cc_final: 0.8024 (pt) REVERT: B 114 PHE cc_start: 0.9063 (t80) cc_final: 0.8803 (t80) REVERT: B 289 MET cc_start: 0.7418 (mmp) cc_final: 0.7144 (mmp) REVERT: B 617 MET cc_start: 0.9275 (mmp) cc_final: 0.8923 (mmm) REVERT: B 683 GLN cc_start: 0.8631 (mp10) cc_final: 0.8290 (mm-40) REVERT: B 696 MET cc_start: 0.6262 (mmm) cc_final: 0.6053 (tpt) REVERT: B 776 MET cc_start: 0.8028 (mtm) cc_final: 0.7726 (mtt) REVERT: B 806 PHE cc_start: 0.8694 (t80) cc_final: 0.8466 (t80) REVERT: A 617 MET cc_start: 0.8754 (mmt) cc_final: 0.8276 (mmm) REVERT: A 663 MET cc_start: 0.9281 (tpp) cc_final: 0.9026 (tpp) REVERT: A 683 GLN cc_start: 0.9263 (mm-40) cc_final: 0.8813 (mm110) REVERT: A 859 LEU cc_start: 0.9274 (tt) cc_final: 0.8843 (mt) REVERT: E 453 LYS cc_start: 0.9570 (mtpp) cc_final: 0.9330 (mmtt) REVERT: E 610 LEU cc_start: 0.9147 (tp) cc_final: 0.8837 (tp) REVERT: E 618 MET cc_start: 0.7766 (mmp) cc_final: 0.7517 (mmm) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.2560 time to fit residues: 63.2756 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 : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 93 optimal weight: 2.9990 chunk 213 optimal weight: 20.0000 chunk 209 optimal weight: 9.9990 chunk 97 optimal weight: 0.4980 chunk 99 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.042808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.031327 restraints weight = 147338.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.032314 restraints weight = 88680.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.032974 restraints weight = 63543.141| |-----------------------------------------------------------------------------| r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 18687 Z= 0.226 Angle : 0.694 9.921 25392 Z= 0.346 Chirality : 0.043 0.240 2945 Planarity : 0.005 0.048 3214 Dihedral : 5.057 59.281 2523 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.05 % Allowed : 1.75 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2287 helix: 1.04 (0.16), residues: 1028 sheet: 0.18 (0.29), residues: 317 loop : -1.20 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 105 HIS 0.008 0.002 HIS E 589 PHE 0.027 0.002 PHE B 524 TYR 0.016 0.002 TYR B 413 ARG 0.005 0.001 ARG B 283 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 2) link_NAG-ASN : angle 2.09228 ( 6) hydrogen bonds : bond 0.04740 ( 879) hydrogen bonds : angle 4.87389 ( 2541) covalent geometry : bond 0.00496 (18685) covalent geometry : angle 0.69368 (25386) *********************** 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 137 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 2.030 Fit side-chains revert: symmetry clash REVERT: B 64 LEU cc_start: 0.8407 (tp) cc_final: 0.8102 (pt) REVERT: B 114 PHE cc_start: 0.9061 (t80) cc_final: 0.8816 (t80) REVERT: B 289 MET cc_start: 0.7456 (mmp) cc_final: 0.7192 (mmp) REVERT: B 392 TYR cc_start: 0.8334 (m-80) cc_final: 0.7989 (m-80) REVERT: B 617 MET cc_start: 0.9289 (mmp) cc_final: 0.8967 (mmm) REVERT: B 664 MET cc_start: 0.8718 (mtm) cc_final: 0.8433 (mtm) REVERT: B 679 PHE cc_start: 0.9138 (t80) cc_final: 0.8929 (t80) REVERT: B 683 GLN cc_start: 0.8526 (mp10) cc_final: 0.8237 (mm-40) REVERT: B 696 MET cc_start: 0.6392 (mmm) cc_final: 0.6117 (tpt) REVERT: B 776 MET cc_start: 0.7856 (mtm) cc_final: 0.7535 (mtt) REVERT: A 76 MET cc_start: 0.8528 (tpt) cc_final: 0.8315 (tpt) REVERT: A 617 MET cc_start: 0.8846 (mmt) cc_final: 0.8342 (mmm) REVERT: A 663 MET cc_start: 0.9291 (tpp) cc_final: 0.9063 (tpp) REVERT: E 453 LYS cc_start: 0.9592 (mtpp) cc_final: 0.9305 (mmtt) REVERT: E 456 MET cc_start: 0.8262 (mmp) cc_final: 0.7355 (tpp) REVERT: E 610 LEU cc_start: 0.9211 (tp) cc_final: 0.8799 (tp) REVERT: E 618 MET cc_start: 0.7885 (mmp) cc_final: 0.7684 (mmm) outliers start: 1 outliers final: 1 residues processed: 137 average time/residue: 0.2433 time to fit residues: 56.6256 Evaluate side-chains 111 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 1.9990 chunk 222 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 203 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 224 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 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 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.043131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.031705 restraints weight = 146794.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.032688 restraints weight = 88341.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.033358 restraints weight = 63306.486| |-----------------------------------------------------------------------------| r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18687 Z= 0.192 Angle : 0.655 10.800 25392 Z= 0.324 Chirality : 0.043 0.241 2945 Planarity : 0.005 0.047 3214 Dihedral : 4.988 59.911 2523 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.17), residues: 2287 helix: 1.05 (0.16), residues: 1040 sheet: 0.11 (0.29), residues: 321 loop : -1.27 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 105 HIS 0.007 0.001 HIS A 101 PHE 0.023 0.002 PHE B 544 TYR 0.015 0.002 TYR B 413 ARG 0.006 0.001 ARG A 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 2) link_NAG-ASN : angle 2.00742 ( 6) hydrogen bonds : bond 0.04515 ( 879) hydrogen bonds : angle 4.80150 ( 2541) covalent geometry : bond 0.00423 (18685) covalent geometry : angle 0.65439 (25386) *********************** 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 135 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 2.066 Fit side-chains revert: symmetry clash REVERT: B 64 LEU cc_start: 0.8415 (tp) cc_final: 0.8112 (pt) REVERT: B 114 PHE cc_start: 0.9086 (t80) cc_final: 0.8834 (t80) REVERT: B 289 MET cc_start: 0.7428 (mmp) cc_final: 0.7171 (mmp) REVERT: B 617 MET cc_start: 0.9292 (mmp) cc_final: 0.8979 (mmm) REVERT: B 679 PHE cc_start: 0.9139 (t80) cc_final: 0.8927 (t80) REVERT: B 683 GLN cc_start: 0.8529 (mp10) cc_final: 0.8247 (mm-40) REVERT: B 696 MET cc_start: 0.6409 (mmm) cc_final: 0.6081 (tpt) REVERT: B 776 MET cc_start: 0.7898 (mtm) cc_final: 0.7622 (mtt) REVERT: A 288 LEU cc_start: 0.9060 (mt) cc_final: 0.8844 (mt) REVERT: A 617 MET cc_start: 0.8795 (mmt) cc_final: 0.8332 (mmm) REVERT: A 663 MET cc_start: 0.9292 (tpp) cc_final: 0.9060 (tpp) REVERT: A 859 LEU cc_start: 0.9314 (tt) cc_final: 0.8878 (mt) REVERT: E 334 MET cc_start: 0.8806 (ptm) cc_final: 0.8401 (ptm) REVERT: E 453 LYS cc_start: 0.9596 (mtpp) cc_final: 0.9312 (mmtt) REVERT: E 456 MET cc_start: 0.8220 (mmp) cc_final: 0.7442 (tpt) REVERT: E 610 LEU cc_start: 0.9194 (tp) cc_final: 0.8892 (tp) REVERT: E 618 MET cc_start: 0.7901 (mmp) cc_final: 0.7684 (mmm) REVERT: E 672 MET cc_start: 0.8175 (mmp) cc_final: 0.7938 (mmm) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2402 time to fit residues: 55.4129 Evaluate side-chains 110 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 118 optimal weight: 5.9990 chunk 130 optimal weight: 0.4980 chunk 134 optimal weight: 0.0970 chunk 110 optimal weight: 8.9990 chunk 177 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 532 HIS ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.044196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.032572 restraints weight = 141563.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.033596 restraints weight = 85806.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.034287 restraints weight = 61370.313| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18687 Z= 0.105 Angle : 0.591 7.598 25392 Z= 0.283 Chirality : 0.041 0.236 2945 Planarity : 0.004 0.048 3214 Dihedral : 4.497 55.867 2523 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.05 % Allowed : 0.10 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.18), residues: 2287 helix: 1.45 (0.17), residues: 1034 sheet: 0.38 (0.30), residues: 319 loop : -1.10 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 105 HIS 0.007 0.001 HIS A 163 PHE 0.021 0.001 PHE B 471 TYR 0.016 0.001 TYR B 413 ARG 0.003 0.000 ARG A 730 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 2) link_NAG-ASN : angle 1.78692 ( 6) hydrogen bonds : bond 0.03849 ( 879) hydrogen bonds : angle 4.42868 ( 2541) covalent geometry : bond 0.00226 (18685) covalent geometry : angle 0.59091 (25386) ********************** 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 146 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 2.020 Fit side-chains revert: symmetry clash REVERT: B 64 LEU cc_start: 0.8376 (tp) cc_final: 0.8084 (pt) REVERT: B 114 PHE cc_start: 0.9100 (t80) cc_final: 0.8856 (t80) REVERT: B 289 MET cc_start: 0.7500 (mmp) cc_final: 0.7279 (mmp) REVERT: B 392 TYR cc_start: 0.8377 (m-80) cc_final: 0.8070 (m-80) REVERT: B 617 MET cc_start: 0.9306 (mmp) cc_final: 0.8923 (mmm) REVERT: B 679 PHE cc_start: 0.8893 (t80) cc_final: 0.8690 (t80) REVERT: B 683 GLN cc_start: 0.8514 (mp10) cc_final: 0.8205 (mm-40) REVERT: B 696 MET cc_start: 0.6301 (mmm) cc_final: 0.6051 (tpt) REVERT: A 288 LEU cc_start: 0.9126 (mt) cc_final: 0.8875 (mt) REVERT: A 559 MET cc_start: 0.8293 (tpt) cc_final: 0.7974 (tpt) REVERT: A 617 MET cc_start: 0.8691 (mmt) cc_final: 0.8197 (mmm) REVERT: A 663 MET cc_start: 0.9259 (tpp) cc_final: 0.9038 (tpp) REVERT: A 675 PHE cc_start: 0.9046 (t80) cc_final: 0.8658 (t80) REVERT: A 683 GLN cc_start: 0.9257 (mm110) cc_final: 0.8771 (mm110) REVERT: A 859 LEU cc_start: 0.9279 (tt) cc_final: 0.8853 (mt) REVERT: E 26 LEU cc_start: 0.8985 (tp) cc_final: 0.8688 (tt) REVERT: E 334 MET cc_start: 0.8727 (ptm) cc_final: 0.8495 (ptm) REVERT: E 453 LYS cc_start: 0.9569 (mtpp) cc_final: 0.9294 (mmtm) REVERT: E 456 MET cc_start: 0.8274 (mmp) cc_final: 0.7499 (tpp) REVERT: E 610 LEU cc_start: 0.9127 (tp) cc_final: 0.8800 (tp) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.2367 time to fit residues: 58.6689 Evaluate side-chains 119 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 175 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 71 optimal weight: 0.0040 chunk 91 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 chunk 186 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 0.0770 chunk 151 optimal weight: 9.9990 overall best weight: 2.2156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS A 330 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.043745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.032232 restraints weight = 143923.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.033230 restraints weight = 87529.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.033911 restraints weight = 62867.036| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18687 Z= 0.133 Angle : 0.596 8.252 25392 Z= 0.290 Chirality : 0.041 0.216 2945 Planarity : 0.005 0.050 3214 Dihedral : 4.475 53.938 2523 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 2287 helix: 1.47 (0.17), residues: 1034 sheet: 0.36 (0.30), residues: 318 loop : -1.07 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 105 HIS 0.005 0.001 HIS A 37 PHE 0.020 0.001 PHE B 471 TYR 0.022 0.001 TYR B 413 ARG 0.004 0.000 ARG A 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 2) link_NAG-ASN : angle 1.69699 ( 6) hydrogen bonds : bond 0.03943 ( 879) hydrogen bonds : angle 4.47357 ( 2541) covalent geometry : bond 0.00296 (18685) covalent geometry : angle 0.59585 (25386) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5294.02 seconds wall clock time: 96 minutes 50.05 seconds (5810.05 seconds total)