Starting phenix.real_space_refine on Wed Mar 4 13:39:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d8z_30615/03_2026/7d8z_30615.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d8z_30615/03_2026/7d8z_30615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7d8z_30615/03_2026/7d8z_30615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d8z_30615/03_2026/7d8z_30615.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d8z_30615/03_2026/7d8z_30615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d8z_30615/03_2026/7d8z_30615.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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 114 5.16 5 C 9006 2.51 5 N 2370 2.21 5 O 2508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13998 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 6943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 6943 Classifications: {'peptide': 895} Link IDs: {'PTRANS': 34, 'TRANS': 860} Chain breaks: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: A, D Time building chain proxies: 6.44, per 1000 atoms: 0.46 Number of scatterers: 13998 At special positions: 0 Unit cell: (114.582, 124.722, 153.114, 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 114 16.00 O 2508 8.00 N 2370 7.00 C 9006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 629 " distance=2.01 Simple disulfide: pdb=" SG CYS B 206 " - pdb=" SG CYS B 591 " distance=2.03 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 325 " distance=2.03 Simple disulfide: pdb=" SG CYS B 345 " - pdb=" SG CYS B 354 " distance=2.04 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 629 " distance=2.01 Simple disulfide: pdb=" SG CYS A 206 " - pdb=" SG CYS A 591 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 325 " distance=2.03 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 354 " distance=2.04 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1201 " - " ASN A 362 " " NAG A1202 " - " ASN A 351 " " NAG B1201 " - " ASN B 362 " " NAG B1202 " - " ASN B 351 " " NAG C 1 " - " ASN B 314 " " NAG D 1 " - " ASN A 314 " Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 606.2 milliseconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 6 sheets defined 59.6% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 98 through 106 removed outlier: 3.777A pdb=" N ALA B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 143 through 151 removed outlier: 3.627A pdb=" N ILE B 149 " --> pdb=" O TRP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 179 removed outlier: 3.621A pdb=" N CYS B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 161 " --> pdb=" O CYS B 157 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS B 165 " --> pdb=" O ILE B 161 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR B 166 " --> pdb=" O CYS B 162 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 229 removed outlier: 3.581A pdb=" N SER B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Proline residue: B 197 - end of helix removed outlier: 3.798A pdb=" N GLY B 201 " --> pdb=" O PRO B 197 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 271 removed outlier: 3.682A pdb=" N MET B 249 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS B 263 " --> pdb=" O CYS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 278 removed outlier: 3.671A pdb=" N LYS B 277 " --> pdb=" O LYS B 273 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 278 " --> pdb=" O TYR B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 303 removed outlier: 3.608A pdb=" N PHE B 282 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 289 " --> pdb=" O CYS B 285 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 345 removed outlier: 3.681A pdb=" N PHE B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 361 removed outlier: 3.501A pdb=" N ASN B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 431 removed outlier: 3.840A pdb=" N LEU B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLY B 428 " --> pdb=" O THR B 424 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 436 through 442 removed outlier: 3.870A pdb=" N SER B 441 " --> pdb=" O MET B 438 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B 442 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 478 removed outlier: 3.811A pdb=" N ILE B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Proline residue: B 455 - end of helix removed outlier: 3.591A pdb=" N THR B 458 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 468 " --> pdb=" O THR B 464 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 486 Processing helix chain 'B' and resid 487 through 494 removed outlier: 4.010A pdb=" N GLY B 490 " --> pdb=" O ASP B 487 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU B 491 " --> pdb=" O LYS B 488 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ALA B 492 " --> pdb=" O PHE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 503 Processing helix chain 'B' and resid 507 through 525 removed outlier: 3.726A pdb=" N VAL B 511 " --> pdb=" O PRO B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 540 removed outlier: 3.564A pdb=" N ARG B 531 " --> pdb=" O THR B 527 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 532 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 550 removed outlier: 3.525A pdb=" N LEU B 545 " --> pdb=" O VAL B 542 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL B 547 " --> pdb=" O PHE B 544 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 548 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS B 550 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 575 removed outlier: 4.022A pdb=" N ILE B 570 " --> pdb=" O CYS B 566 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B 571 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 605 removed outlier: 3.526A pdb=" N ALA B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Proline residue: B 582 - end of helix removed outlier: 3.775A pdb=" N PHE B 587 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS B 599 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR B 603 " --> pdb=" O CYS B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 637 removed outlier: 3.752A pdb=" N GLY B 625 " --> pdb=" O LEU B 621 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET B 633 " --> pdb=" O CYS B 629 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER B 637 " --> pdb=" O MET B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 664 removed outlier: 4.554A pdb=" N VAL B 643 " --> pdb=" O TYR B 639 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 647 " --> pdb=" O VAL B 643 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS B 653 " --> pdb=" O GLY B 649 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU B 656 " --> pdb=" O TYR B 652 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B 661 " --> pdb=" O TYR B 657 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS B 662 " --> pdb=" O ARG B 658 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU B 663 " --> pdb=" O GLY B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 683 removed outlier: 3.677A pdb=" N ALA B 675 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 722 removed outlier: 4.116A pdb=" N LEU B 715 " --> pdb=" O HIS B 711 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 718 " --> pdb=" O LEU B 714 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER B 719 " --> pdb=" O LEU B 715 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 720 " --> pdb=" O SER B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 740 Processing helix chain 'B' and resid 741 through 759 removed outlier: 3.933A pdb=" N ILE B 752 " --> pdb=" O ALA B 748 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 755 " --> pdb=" O SER B 751 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B 757 " --> pdb=" O ARG B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 779 removed outlier: 3.518A pdb=" N GLY B 776 " --> pdb=" O ASN B 772 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER B 778 " --> pdb=" O ARG B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 825 removed outlier: 3.530A pdb=" N PHE B 814 " --> pdb=" O THR B 810 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 815 " --> pdb=" O TRP B 811 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 819 " --> pdb=" O ILE B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 862 Processing helix chain 'B' and resid 862 through 870 removed outlier: 4.087A pdb=" N PHE B 866 " --> pdb=" O MET B 862 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS B 870 " --> pdb=" O PHE B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 905 removed outlier: 3.828A pdb=" N THR B 899 " --> pdb=" O LYS B 895 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 900 " --> pdb=" O LYS B 896 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE B 901 " --> pdb=" O ASP B 897 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 902 " --> pdb=" O LEU B 898 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 903 " --> pdb=" O THR B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 1068 through 1085 removed outlier: 3.672A pdb=" N THR B1075 " --> pdb=" O ARG B1071 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL B1077 " --> pdb=" O MET B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1111 through 1118 Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 98 through 106 removed outlier: 3.777A pdb=" N ALA A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 143 through 151 removed outlier: 3.627A pdb=" N ILE A 149 " --> pdb=" O TRP A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 179 removed outlier: 3.621A pdb=" N CYS A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 161 " --> pdb=" O CYS A 157 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR A 166 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 229 removed outlier: 3.581A pdb=" N SER A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Proline residue: A 197 - end of helix removed outlier: 3.798A pdb=" N GLY A 201 " --> pdb=" O PRO A 197 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 271 removed outlier: 3.682A pdb=" N MET A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS A 263 " --> pdb=" O CYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.671A pdb=" N LYS A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 303 removed outlier: 3.608A pdb=" N PHE A 282 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 289 " --> pdb=" O CYS A 285 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 298 " --> pdb=" O TYR A 294 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 3.681A pdb=" N PHE A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 361 removed outlier: 3.501A pdb=" N ASN A 361 " --> pdb=" O TYR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 431 removed outlier: 3.840A pdb=" N LEU A 426 " --> pdb=" O TYR A 422 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLY A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 436 through 442 removed outlier: 3.870A pdb=" N SER A 441 " --> pdb=" O MET A 438 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN A 442 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 478 removed outlier: 3.811A pdb=" N ILE A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Proline residue: A 455 - end of helix removed outlier: 3.591A pdb=" N THR A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 468 " --> pdb=" O THR A 464 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 486 Processing helix chain 'A' and resid 487 through 494 removed outlier: 4.010A pdb=" N GLY A 490 " --> pdb=" O ASP A 487 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU A 491 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ALA A 492 " --> pdb=" O PHE A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 507 through 525 removed outlier: 3.726A pdb=" N VAL A 511 " --> pdb=" O PRO A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 540 removed outlier: 3.564A pdb=" N ARG A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 532 " --> pdb=" O GLY A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 550 removed outlier: 3.525A pdb=" N LEU A 545 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL A 547 " --> pdb=" O PHE A 544 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 548 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 550 " --> pdb=" O VAL A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 removed outlier: 4.022A pdb=" N ILE A 570 " --> pdb=" O CYS A 566 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 605 removed outlier: 3.526A pdb=" N ALA A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Proline residue: A 582 - end of helix removed outlier: 3.775A pdb=" N PHE A 587 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS A 599 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 603 " --> pdb=" O CYS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 637 removed outlier: 3.752A pdb=" N GLY A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET A 633 " --> pdb=" O CYS A 629 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 637 " --> pdb=" O MET A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 664 removed outlier: 4.554A pdb=" N VAL A 643 " --> pdb=" O TYR A 639 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 647 " --> pdb=" O VAL A 643 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 653 " --> pdb=" O GLY A 649 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU A 656 " --> pdb=" O TYR A 652 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU A 661 " --> pdb=" O TYR A 657 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 662 " --> pdb=" O ARG A 658 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 683 removed outlier: 3.677A pdb=" N ALA A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 722 removed outlier: 4.116A pdb=" N LEU A 715 " --> pdb=" O HIS A 711 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 720 " --> pdb=" O SER A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 740 Processing helix chain 'A' and resid 741 through 759 removed outlier: 3.933A pdb=" N ILE A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 755 " --> pdb=" O SER A 751 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 757 " --> pdb=" O ARG A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 779 removed outlier: 3.518A pdb=" N GLY A 776 " --> pdb=" O ASN A 772 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 825 removed outlier: 3.530A pdb=" N PHE A 814 " --> pdb=" O THR A 810 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 815 " --> pdb=" O TRP A 811 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 819 " --> pdb=" O ILE A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 862 Processing helix chain 'A' and resid 862 through 870 removed outlier: 4.087A pdb=" N PHE A 866 " --> pdb=" O MET A 862 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS A 870 " --> pdb=" O PHE A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 905 removed outlier: 3.828A pdb=" N THR A 899 " --> pdb=" O LYS A 895 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 900 " --> pdb=" O LYS A 896 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE A 901 " --> pdb=" O ASP A 897 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 902 " --> pdb=" O LEU A 898 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 903 " --> pdb=" O THR A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1085 removed outlier: 3.672A pdb=" N THR A1075 " --> pdb=" O ARG A1071 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A1077 " --> pdb=" O MET A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1118 Processing sheet with id=AA1, first strand: chain 'B' and resid 315 through 316 Processing sheet with id=AA2, first strand: chain 'B' and resid 328 through 331 Processing sheet with id=AA3, first strand: chain 'B' and resid 764 through 770 removed outlier: 6.552A pdb=" N VAL B 730 " --> pdb=" O GLN B 766 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL B 768 " --> pdb=" O VAL B 730 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER B 732 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N SER B 770 " --> pdb=" O SER B 732 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU B 734 " --> pdb=" O SER B 770 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU B 697 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLY B 731 " --> pdb=" O LEU B 697 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 699 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N VAL B 733 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL B 701 " --> pdb=" O VAL B 733 " (cutoff:3.500A) removed outlier: 10.370A pdb=" N GLU B 735 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU B 698 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL B1124 " --> pdb=" O LYS B 832 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL B1093 " --> pdb=" O MET B1125 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL B1127 " --> pdb=" O VAL B1093 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU B1095 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N GLY B1129 " --> pdb=" O LEU B1095 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER B 848 " --> pdb=" O LEU B1092 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N LEU B1094 " --> pdb=" O SER B 848 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASP B 850 " --> pdb=" O LEU B1094 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N ASN B1096 " --> pdb=" O ASP B 850 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N TRP B 852 " --> pdb=" O ASN B1096 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 315 through 316 Processing sheet with id=AA5, first strand: chain 'A' and resid 328 through 331 Processing sheet with id=AA6, first strand: chain 'A' and resid 764 through 770 removed outlier: 6.552A pdb=" N VAL A 730 " --> pdb=" O GLN A 766 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL A 768 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER A 732 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N SER A 770 " --> pdb=" O SER A 732 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU A 734 " --> pdb=" O SER A 770 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU A 697 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLY A 731 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL A 699 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N VAL A 733 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL A 701 " --> pdb=" O VAL A 733 " (cutoff:3.500A) removed outlier: 10.370A pdb=" N GLU A 735 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU A 698 " --> pdb=" O LEU A 795 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL A1124 " --> pdb=" O LYS A 832 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A1093 " --> pdb=" O MET A1125 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL A1127 " --> pdb=" O VAL A1093 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU A1095 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N GLY A1129 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER A 848 " --> pdb=" O LEU A1092 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N LEU A1094 " --> pdb=" O SER A 848 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASP A 850 " --> pdb=" O LEU A1094 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N ASN A1096 " --> pdb=" O ASP A 850 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N TRP A 852 " --> pdb=" O ASN A1096 " (cutoff:3.500A) 627 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4448 1.34 - 1.47: 3534 1.47 - 1.59: 6144 1.59 - 1.71: 0 1.71 - 1.84: 182 Bond restraints: 14308 Sorted by residual: bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" CA THR B 435 " pdb=" CB THR B 435 " ideal model delta sigma weight residual 1.532 1.492 0.039 1.74e-02 3.30e+03 5.05e+00 bond pdb=" CA THR A 435 " pdb=" CB THR A 435 " ideal model delta sigma weight residual 1.532 1.492 0.039 1.74e-02 3.30e+03 5.05e+00 bond pdb=" CA ASP B 807 " pdb=" C ASP B 807 " ideal model delta sigma weight residual 1.523 1.552 -0.029 1.34e-02 5.57e+03 4.75e+00 ... (remaining 14303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 18616 2.50 - 5.00: 662 5.00 - 7.49: 110 7.49 - 9.99: 22 9.99 - 12.49: 4 Bond angle restraints: 19414 Sorted by residual: angle pdb=" N GLN B 707 " pdb=" CA GLN B 707 " pdb=" C GLN B 707 " ideal model delta sigma weight residual 110.24 122.73 -12.49 1.47e+00 4.63e-01 7.22e+01 angle pdb=" N GLN A 707 " pdb=" CA GLN A 707 " pdb=" C GLN A 707 " ideal model delta sigma weight residual 110.24 122.73 -12.49 1.47e+00 4.63e-01 7.22e+01 angle pdb=" N ASP A 706 " pdb=" CA ASP A 706 " pdb=" C ASP A 706 " ideal model delta sigma weight residual 111.24 99.95 11.29 1.38e+00 5.25e-01 6.70e+01 angle pdb=" N ASP B 706 " pdb=" CA ASP B 706 " pdb=" C ASP B 706 " ideal model delta sigma weight residual 111.24 99.95 11.29 1.38e+00 5.25e-01 6.70e+01 angle pdb=" N VAL A 181 " pdb=" CA VAL A 181 " pdb=" C VAL A 181 " ideal model delta sigma weight residual 112.43 106.76 5.67 9.20e-01 1.18e+00 3.80e+01 ... (remaining 19409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 8040 15.43 - 30.86: 382 30.86 - 46.29: 98 46.29 - 61.73: 14 61.73 - 77.16: 8 Dihedral angle restraints: 8542 sinusoidal: 3444 harmonic: 5098 Sorted by residual: dihedral pdb=" CB CYS B 165 " pdb=" SG CYS B 165 " pdb=" SG CYS B 629 " pdb=" CB CYS B 629 " ideal model delta sinusoidal sigma weight residual -86.00 -151.86 65.86 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS A 165 " pdb=" SG CYS A 165 " pdb=" SG CYS A 629 " pdb=" CB CYS A 629 " ideal model delta sinusoidal sigma weight residual -86.00 -151.86 65.86 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS A 206 " pdb=" SG CYS A 206 " pdb=" SG CYS A 591 " pdb=" CB CYS A 591 " ideal model delta sinusoidal sigma weight residual 93.00 153.65 -60.65 1 1.00e+01 1.00e-02 4.89e+01 ... (remaining 8539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 2094 0.109 - 0.218: 140 0.218 - 0.327: 10 0.327 - 0.436: 2 0.436 - 0.545: 2 Chirality restraints: 2248 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 314 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.94 0.54 2.00e-01 2.50e+01 7.41e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN B 314 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.94 0.54 2.00e-01 2.50e+01 7.41e+00 chirality pdb=" CA GLN A 707 " pdb=" N GLN A 707 " pdb=" C GLN A 707 " pdb=" CB GLN A 707 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.41e+00 ... (remaining 2245 not shown) Planarity restraints: 2436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 128 " 0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO A 129 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 128 " -0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO B 129 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 506 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO B 507 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 507 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 507 " 0.031 5.00e-02 4.00e+02 ... (remaining 2433 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2262 2.75 - 3.29: 13336 3.29 - 3.82: 22103 3.82 - 4.36: 26367 4.36 - 4.90: 44572 Nonbonded interactions: 108640 Sorted by model distance: nonbonded pdb=" O GLN A 707 " pdb=" OD1 ASN A 708 " model vdw 2.209 3.040 nonbonded pdb=" O GLN B 707 " pdb=" OD1 ASN B 708 " model vdw 2.209 3.040 nonbonded pdb=" O HIS A 779 " pdb=" OG SER A 783 " model vdw 2.240 3.040 nonbonded pdb=" O HIS B 779 " pdb=" OG SER B 783 " model vdw 2.240 3.040 nonbonded pdb=" OG1 THR B 607 " pdb=" OH TYR B 678 " model vdw 2.255 3.040 ... (remaining 108635 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.990 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 : 0.009 0.079 14324 Z= 0.376 Angle : 1.206 21.971 19454 Z= 0.663 Chirality : 0.062 0.545 2248 Planarity : 0.007 0.055 2430 Dihedral : 10.330 77.158 5258 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.22 % Favored : 90.66 % Rotamer: Outliers : 0.53 % Allowed : 3.60 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.56 (0.13), residues: 1778 helix: -4.09 (0.09), residues: 926 sheet: -0.92 (0.36), residues: 168 loop : -3.60 (0.17), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 315 TYR 0.023 0.003 TYR A 189 PHE 0.032 0.003 PHE B 416 TRP 0.020 0.003 TRP A 382 HIS 0.016 0.003 HIS A 808 Details of bonding type rmsd covalent geometry : bond 0.00856 (14308) covalent geometry : angle 1.14808 (19414) SS BOND : bond 0.01355 ( 8) SS BOND : angle 2.90720 ( 16) hydrogen bonds : bond 0.30944 ( 627) hydrogen bonds : angle 10.32120 ( 1809) link_BETA1-4 : bond 0.00383 ( 2) link_BETA1-4 : angle 7.51549 ( 6) link_NAG-ASN : bond 0.02438 ( 6) link_NAG-ASN : angle 11.07526 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 367 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 353 THR cc_start: 0.6861 (p) cc_final: 0.6584 (t) REVERT: B 524 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7925 (tm-30) REVERT: B 727 LEU cc_start: 0.8646 (tp) cc_final: 0.8274 (tp) REVERT: B 760 LYS cc_start: 0.7937 (mptt) cc_final: 0.7690 (mmmt) REVERT: B 836 MET cc_start: 0.8070 (ptm) cc_final: 0.7822 (ptm) REVERT: A 353 THR cc_start: 0.6855 (p) cc_final: 0.6585 (t) REVERT: A 524 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7931 (tm-30) REVERT: A 727 LEU cc_start: 0.8656 (tp) cc_final: 0.8285 (tp) REVERT: A 760 LYS cc_start: 0.7935 (mptt) cc_final: 0.7691 (mmmt) REVERT: A 836 MET cc_start: 0.8064 (ptm) cc_final: 0.7811 (ptm) outliers start: 8 outliers final: 2 residues processed: 373 average time/residue: 0.1542 time to fit residues: 78.2889 Evaluate side-chains 211 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain A residue 126 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 HIS ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 HIS B 808 HIS B 871 HIS B1096 ASN A 618 HIS ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 HIS A 808 HIS A 871 HIS A1096 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.118652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097309 restraints weight = 31956.085| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.98 r_work: 0.3406 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14324 Z= 0.160 Angle : 0.766 9.282 19454 Z= 0.390 Chirality : 0.046 0.262 2248 Planarity : 0.006 0.051 2430 Dihedral : 7.354 53.562 2104 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.67 % Allowed : 10.67 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.77 (0.16), residues: 1778 helix: -2.23 (0.13), residues: 960 sheet: -0.46 (0.39), residues: 154 loop : -3.28 (0.19), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 348 TYR 0.028 0.002 TYR B 414 PHE 0.020 0.002 PHE A 156 TRP 0.016 0.001 TRP B 693 HIS 0.012 0.002 HIS A1074 Details of bonding type rmsd covalent geometry : bond 0.00342 (14308) covalent geometry : angle 0.74793 (19414) SS BOND : bond 0.00828 ( 8) SS BOND : angle 3.53263 ( 16) hydrogen bonds : bond 0.05963 ( 627) hydrogen bonds : angle 5.54742 ( 1809) link_BETA1-4 : bond 0.00302 ( 2) link_BETA1-4 : angle 4.28658 ( 6) link_NAG-ASN : bond 0.00267 ( 6) link_NAG-ASN : angle 3.63236 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 262 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 PHE cc_start: 0.8223 (t80) cc_final: 0.7994 (t80) REVERT: B 727 LEU cc_start: 0.8635 (tp) cc_final: 0.8117 (tp) REVERT: B 800 ARG cc_start: 0.8060 (mmm160) cc_final: 0.7391 (tpp80) REVERT: B 864 LEU cc_start: 0.8852 (mm) cc_final: 0.8642 (mm) REVERT: B 879 MET cc_start: 0.8020 (ttm) cc_final: 0.7799 (ttm) REVERT: A 160 PHE cc_start: 0.8217 (t80) cc_final: 0.7989 (t80) REVERT: A 727 LEU cc_start: 0.8646 (tp) cc_final: 0.8152 (tp) REVERT: A 800 ARG cc_start: 0.8076 (mmm160) cc_final: 0.7381 (tpp80) REVERT: A 864 LEU cc_start: 0.8852 (mm) cc_final: 0.8644 (mm) REVERT: A 879 MET cc_start: 0.8023 (ttm) cc_final: 0.7796 (ttm) outliers start: 25 outliers final: 15 residues processed: 277 average time/residue: 0.1081 time to fit residues: 44.6672 Evaluate side-chains 206 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 872 LYS Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 170 optimal weight: 0.0270 chunk 62 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 chunk 14 optimal weight: 0.1980 chunk 87 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 chunk 15 optimal weight: 0.0670 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 ASN B 361 ASN ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1096 ASN A 133 ASN A 361 ASN A 494 ASN ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.120650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.098991 restraints weight = 32066.862| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.04 r_work: 0.3436 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14324 Z= 0.124 Angle : 0.658 7.702 19454 Z= 0.332 Chirality : 0.044 0.203 2248 Planarity : 0.004 0.040 2430 Dihedral : 6.642 49.839 2104 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.60 % Allowed : 11.27 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.18), residues: 1778 helix: -1.17 (0.15), residues: 972 sheet: -0.70 (0.37), residues: 168 loop : -3.08 (0.20), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 880 TYR 0.013 0.001 TYR A 430 PHE 0.024 0.001 PHE B 207 TRP 0.019 0.001 TRP A 693 HIS 0.004 0.001 HIS A 904 Details of bonding type rmsd covalent geometry : bond 0.00266 (14308) covalent geometry : angle 0.64600 (19414) SS BOND : bond 0.00448 ( 8) SS BOND : angle 1.91966 ( 16) hydrogen bonds : bond 0.04473 ( 627) hydrogen bonds : angle 4.83790 ( 1809) link_BETA1-4 : bond 0.00319 ( 2) link_BETA1-4 : angle 4.11419 ( 6) link_NAG-ASN : bond 0.00469 ( 6) link_NAG-ASN : angle 2.91210 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 160 PHE cc_start: 0.8255 (t80) cc_final: 0.8017 (t80) REVERT: B 578 ASP cc_start: 0.7163 (p0) cc_final: 0.6933 (p0) REVERT: B 593 MET cc_start: 0.8427 (tpt) cc_final: 0.7994 (ttp) REVERT: B 727 LEU cc_start: 0.8623 (tp) cc_final: 0.8372 (tp) REVERT: B 789 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7623 (pp) REVERT: B 800 ARG cc_start: 0.8058 (mmm160) cc_final: 0.7398 (tpp80) REVERT: B 863 LEU cc_start: 0.8991 (tp) cc_final: 0.8708 (tp) REVERT: B 864 LEU cc_start: 0.8878 (mm) cc_final: 0.8630 (mm) REVERT: B 907 ILE cc_start: 0.5165 (OUTLIER) cc_final: 0.4943 (mp) REVERT: A 160 PHE cc_start: 0.8240 (t80) cc_final: 0.7999 (t80) REVERT: A 578 ASP cc_start: 0.7252 (p0) cc_final: 0.7031 (p0) REVERT: A 583 ILE cc_start: 0.8634 (mt) cc_final: 0.8365 (mt) REVERT: A 593 MET cc_start: 0.8414 (tpt) cc_final: 0.7994 (ttp) REVERT: A 727 LEU cc_start: 0.8610 (tp) cc_final: 0.8361 (tp) REVERT: A 789 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7623 (pp) REVERT: A 800 ARG cc_start: 0.8062 (mmm160) cc_final: 0.7383 (tpp80) REVERT: A 863 LEU cc_start: 0.8987 (tp) cc_final: 0.8707 (tp) REVERT: A 864 LEU cc_start: 0.8884 (mm) cc_final: 0.8637 (mm) REVERT: A 907 ILE cc_start: 0.5177 (OUTLIER) cc_final: 0.4955 (mp) outliers start: 39 outliers final: 21 residues processed: 245 average time/residue: 0.1073 time to fit residues: 40.3834 Evaluate side-chains 224 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 TRP Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 105 optimal weight: 0.1980 chunk 21 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 ASN B 494 ASN ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.119928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.099049 restraints weight = 31608.546| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.93 r_work: 0.3444 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14324 Z= 0.116 Angle : 0.626 7.863 19454 Z= 0.313 Chirality : 0.042 0.187 2248 Planarity : 0.004 0.039 2430 Dihedral : 6.055 52.451 2104 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.73 % Allowed : 12.00 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.18), residues: 1778 helix: -0.64 (0.16), residues: 964 sheet: -0.46 (0.37), residues: 164 loop : -3.01 (0.20), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 348 TYR 0.007 0.001 TYR A 639 PHE 0.028 0.001 PHE B 207 TRP 0.011 0.001 TRP B 693 HIS 0.003 0.001 HIS B 904 Details of bonding type rmsd covalent geometry : bond 0.00260 (14308) covalent geometry : angle 0.61576 (19414) SS BOND : bond 0.00252 ( 8) SS BOND : angle 1.54895 ( 16) hydrogen bonds : bond 0.03828 ( 627) hydrogen bonds : angle 4.53786 ( 1809) link_BETA1-4 : bond 0.00362 ( 2) link_BETA1-4 : angle 3.57802 ( 6) link_NAG-ASN : bond 0.00319 ( 6) link_NAG-ASN : angle 2.94981 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 234 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 PHE cc_start: 0.8255 (t80) cc_final: 0.8007 (t80) REVERT: B 727 LEU cc_start: 0.8649 (tp) cc_final: 0.8408 (tp) REVERT: B 789 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7559 (pp) REVERT: B 800 ARG cc_start: 0.8029 (mmm160) cc_final: 0.7463 (tpp80) REVERT: B 863 LEU cc_start: 0.9011 (tp) cc_final: 0.8699 (tp) REVERT: B 864 LEU cc_start: 0.8921 (mm) cc_final: 0.8585 (mm) REVERT: B 907 ILE cc_start: 0.5179 (OUTLIER) cc_final: 0.4856 (mp) REVERT: A 160 PHE cc_start: 0.8261 (t80) cc_final: 0.8009 (t80) REVERT: A 583 ILE cc_start: 0.8617 (mt) cc_final: 0.8363 (mt) REVERT: A 727 LEU cc_start: 0.8628 (tp) cc_final: 0.8424 (tp) REVERT: A 789 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7564 (pp) REVERT: A 863 LEU cc_start: 0.9009 (tp) cc_final: 0.8698 (tp) REVERT: A 864 LEU cc_start: 0.8926 (mm) cc_final: 0.8587 (mm) REVERT: A 907 ILE cc_start: 0.5193 (OUTLIER) cc_final: 0.4988 (mp) REVERT: A 1074 HIS cc_start: 0.8522 (OUTLIER) cc_final: 0.8295 (t-90) outliers start: 56 outliers final: 29 residues processed: 266 average time/residue: 0.1107 time to fit residues: 45.0770 Evaluate side-chains 230 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 TRP Chi-restraints excluded: chain B residue 837 PHE Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1074 HIS Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 123 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 167 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 602 GLN ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 HIS B1096 ASN A 602 GLN ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.119598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.098416 restraints weight = 32563.233| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.99 r_work: 0.3430 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14324 Z= 0.124 Angle : 0.617 6.438 19454 Z= 0.308 Chirality : 0.043 0.256 2248 Planarity : 0.003 0.038 2430 Dihedral : 5.793 42.666 2104 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.60 % Allowed : 14.87 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.18), residues: 1778 helix: -0.35 (0.16), residues: 980 sheet: -0.28 (0.38), residues: 164 loop : -2.94 (0.20), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 348 TYR 0.010 0.001 TYR A 430 PHE 0.029 0.001 PHE B 207 TRP 0.016 0.001 TRP B 798 HIS 0.002 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00286 (14308) covalent geometry : angle 0.60714 (19414) SS BOND : bond 0.00221 ( 8) SS BOND : angle 1.60819 ( 16) hydrogen bonds : bond 0.03711 ( 627) hydrogen bonds : angle 4.40278 ( 1809) link_BETA1-4 : bond 0.00303 ( 2) link_BETA1-4 : angle 3.30730 ( 6) link_NAG-ASN : bond 0.00476 ( 6) link_NAG-ASN : angle 2.92530 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 PHE cc_start: 0.8270 (t80) cc_final: 0.8014 (t80) REVERT: B 727 LEU cc_start: 0.8671 (tp) cc_final: 0.8442 (tp) REVERT: B 789 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7616 (pp) REVERT: B 863 LEU cc_start: 0.9037 (tp) cc_final: 0.8772 (tp) REVERT: B 907 ILE cc_start: 0.5352 (OUTLIER) cc_final: 0.5036 (mp) REVERT: A 160 PHE cc_start: 0.8263 (t80) cc_final: 0.8011 (t80) REVERT: A 583 ILE cc_start: 0.8624 (mt) cc_final: 0.8362 (mt) REVERT: A 789 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7625 (pp) REVERT: A 800 ARG cc_start: 0.8157 (mmm160) cc_final: 0.7456 (ttm170) REVERT: A 863 LEU cc_start: 0.9045 (tp) cc_final: 0.8773 (tp) REVERT: A 864 LEU cc_start: 0.8931 (mm) cc_final: 0.8696 (mm) REVERT: A 907 ILE cc_start: 0.5361 (OUTLIER) cc_final: 0.5032 (mp) outliers start: 54 outliers final: 36 residues processed: 242 average time/residue: 0.1138 time to fit residues: 41.3744 Evaluate side-chains 239 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 TRP Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 13 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 chunk 9 optimal weight: 0.0470 chunk 106 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 177 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 HIS ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.120307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.099672 restraints weight = 31691.039| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.92 r_work: 0.3452 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14324 Z= 0.112 Angle : 0.612 9.613 19454 Z= 0.303 Chirality : 0.042 0.200 2248 Planarity : 0.003 0.037 2430 Dihedral : 5.608 48.910 2104 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.47 % Allowed : 14.93 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.19), residues: 1778 helix: -0.05 (0.16), residues: 974 sheet: 0.08 (0.39), residues: 160 loop : -2.92 (0.20), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1078 TYR 0.007 0.001 TYR A 430 PHE 0.033 0.001 PHE B 207 TRP 0.014 0.001 TRP B 811 HIS 0.002 0.001 HIS B 904 Details of bonding type rmsd covalent geometry : bond 0.00254 (14308) covalent geometry : angle 0.60200 (19414) SS BOND : bond 0.00205 ( 8) SS BOND : angle 1.44122 ( 16) hydrogen bonds : bond 0.03465 ( 627) hydrogen bonds : angle 4.23034 ( 1809) link_BETA1-4 : bond 0.00324 ( 2) link_BETA1-4 : angle 3.29914 ( 6) link_NAG-ASN : bond 0.00391 ( 6) link_NAG-ASN : angle 2.82158 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 213 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 PHE cc_start: 0.8235 (t80) cc_final: 0.7981 (t80) REVERT: B 727 LEU cc_start: 0.8733 (tp) cc_final: 0.8522 (tp) REVERT: B 789 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7524 (pp) REVERT: B 800 ARG cc_start: 0.8107 (mmm160) cc_final: 0.7423 (tpp80) REVERT: B 863 LEU cc_start: 0.9027 (tp) cc_final: 0.8753 (tp) REVERT: B 907 ILE cc_start: 0.5328 (OUTLIER) cc_final: 0.5124 (mp) REVERT: A 160 PHE cc_start: 0.8247 (t80) cc_final: 0.7993 (t80) REVERT: A 583 ILE cc_start: 0.8586 (mt) cc_final: 0.8341 (mt) REVERT: A 789 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7576 (pp) REVERT: A 800 ARG cc_start: 0.8179 (mmm160) cc_final: 0.7654 (tpp80) REVERT: A 863 LEU cc_start: 0.9028 (tp) cc_final: 0.8751 (tp) REVERT: A 907 ILE cc_start: 0.5335 (OUTLIER) cc_final: 0.5130 (mp) outliers start: 52 outliers final: 35 residues processed: 245 average time/residue: 0.1059 time to fit residues: 39.5779 Evaluate side-chains 234 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 TRP Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 872 LYS Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 59 optimal weight: 10.0000 chunk 45 optimal weight: 0.0570 chunk 143 optimal weight: 0.6980 chunk 88 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1096 ASN ** A 779 HIS ** 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 = 0.3871 r_free = 0.3871 target = 0.120918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.100321 restraints weight = 31530.699| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.89 r_work: 0.3460 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14324 Z= 0.113 Angle : 0.631 12.663 19454 Z= 0.309 Chirality : 0.042 0.245 2248 Planarity : 0.003 0.065 2430 Dihedral : 5.548 48.435 2104 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.80 % Allowed : 15.47 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.19), residues: 1778 helix: 0.14 (0.17), residues: 976 sheet: 0.19 (0.39), residues: 160 loop : -2.86 (0.21), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 348 TYR 0.007 0.001 TYR A 430 PHE 0.027 0.001 PHE A 207 TRP 0.014 0.001 TRP B 811 HIS 0.002 0.001 HIS B1120 Details of bonding type rmsd covalent geometry : bond 0.00251 (14308) covalent geometry : angle 0.62164 (19414) SS BOND : bond 0.00190 ( 8) SS BOND : angle 1.43093 ( 16) hydrogen bonds : bond 0.03373 ( 627) hydrogen bonds : angle 4.15362 ( 1809) link_BETA1-4 : bond 0.00238 ( 2) link_BETA1-4 : angle 3.30421 ( 6) link_NAG-ASN : bond 0.00308 ( 6) link_NAG-ASN : angle 2.80951 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 203 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 PHE cc_start: 0.8250 (t80) cc_final: 0.7999 (t80) REVERT: B 410 MET cc_start: 0.7914 (ppp) cc_final: 0.7488 (ppp) REVERT: B 789 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7495 (pp) REVERT: B 800 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7460 (tpp80) REVERT: B 862 MET cc_start: 0.8751 (mmt) cc_final: 0.8495 (mpp) REVERT: B 863 LEU cc_start: 0.9011 (tp) cc_final: 0.8724 (tp) REVERT: A 160 PHE cc_start: 0.8243 (t80) cc_final: 0.7991 (t80) REVERT: A 583 ILE cc_start: 0.8565 (mt) cc_final: 0.8334 (mt) REVERT: A 789 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7578 (pp) REVERT: A 800 ARG cc_start: 0.8137 (mmm160) cc_final: 0.7646 (tpp80) REVERT: A 862 MET cc_start: 0.8775 (mmt) cc_final: 0.8524 (mpp) REVERT: A 863 LEU cc_start: 0.9014 (tp) cc_final: 0.8726 (tp) REVERT: A 907 ILE cc_start: 0.5405 (OUTLIER) cc_final: 0.5204 (mp) outliers start: 42 outliers final: 35 residues processed: 227 average time/residue: 0.1061 time to fit residues: 36.3438 Evaluate side-chains 230 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 TRP Chi-restraints excluded: chain B residue 872 LYS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 47 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 167 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 174 optimal weight: 0.3980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 442 ASN ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** 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 = 0.3835 r_free = 0.3835 target = 0.118587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.097707 restraints weight = 31681.096| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.91 r_work: 0.3414 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14324 Z= 0.141 Angle : 0.658 9.507 19454 Z= 0.325 Chirality : 0.043 0.218 2248 Planarity : 0.003 0.041 2430 Dihedral : 5.490 38.954 2104 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.73 % Allowed : 15.00 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.19), residues: 1778 helix: 0.21 (0.17), residues: 966 sheet: 0.10 (0.40), residues: 164 loop : -2.73 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 348 TYR 0.009 0.001 TYR B 617 PHE 0.024 0.001 PHE B 207 TRP 0.013 0.001 TRP B 811 HIS 0.012 0.001 HIS A1074 Details of bonding type rmsd covalent geometry : bond 0.00335 (14308) covalent geometry : angle 0.64850 (19414) SS BOND : bond 0.00258 ( 8) SS BOND : angle 1.68557 ( 16) hydrogen bonds : bond 0.03563 ( 627) hydrogen bonds : angle 4.19136 ( 1809) link_BETA1-4 : bond 0.00199 ( 2) link_BETA1-4 : angle 3.16128 ( 6) link_NAG-ASN : bond 0.00262 ( 6) link_NAG-ASN : angle 2.83677 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 191 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 PHE cc_start: 0.8305 (t80) cc_final: 0.8058 (t80) REVERT: B 410 MET cc_start: 0.7920 (ppp) cc_final: 0.7389 (ttt) REVERT: B 583 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8200 (mt) REVERT: B 626 MET cc_start: 0.8422 (tpp) cc_final: 0.7874 (tpp) REVERT: B 725 LYS cc_start: 0.7788 (mttt) cc_final: 0.7586 (mmtt) REVERT: B 789 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7656 (pp) REVERT: B 800 ARG cc_start: 0.8178 (mmm160) cc_final: 0.7652 (tpp80) REVERT: B 863 LEU cc_start: 0.8974 (tp) cc_final: 0.8666 (tp) REVERT: A 160 PHE cc_start: 0.8319 (t80) cc_final: 0.8079 (t80) REVERT: A 583 ILE cc_start: 0.8508 (mt) cc_final: 0.8290 (mt) REVERT: A 626 MET cc_start: 0.8354 (tpp) cc_final: 0.7837 (tpp) REVERT: A 789 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7715 (pp) REVERT: A 863 LEU cc_start: 0.8994 (tp) cc_final: 0.8697 (tp) REVERT: A 907 ILE cc_start: 0.5448 (OUTLIER) cc_final: 0.5231 (mp) outliers start: 56 outliers final: 43 residues processed: 232 average time/residue: 0.1159 time to fit residues: 39.9902 Evaluate side-chains 231 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 184 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 TRP Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 872 LYS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 20 optimal weight: 6.9990 chunk 21 optimal weight: 0.0270 chunk 39 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 162 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 2 optimal weight: 0.0570 chunk 114 optimal weight: 0.0980 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.120316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.099640 restraints weight = 31601.180| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.89 r_work: 0.3443 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14324 Z= 0.113 Angle : 0.645 15.116 19454 Z= 0.313 Chirality : 0.042 0.189 2248 Planarity : 0.003 0.037 2430 Dihedral : 5.326 38.070 2104 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.67 % Allowed : 15.80 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.19), residues: 1778 helix: 0.32 (0.17), residues: 974 sheet: 0.16 (0.40), residues: 164 loop : -2.81 (0.20), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 348 TYR 0.006 0.001 TYR A 430 PHE 0.036 0.001 PHE B 207 TRP 0.014 0.001 TRP B 811 HIS 0.007 0.001 HIS A1074 Details of bonding type rmsd covalent geometry : bond 0.00258 (14308) covalent geometry : angle 0.63610 (19414) SS BOND : bond 0.00194 ( 8) SS BOND : angle 1.42089 ( 16) hydrogen bonds : bond 0.03380 ( 627) hydrogen bonds : angle 4.08060 ( 1809) link_BETA1-4 : bond 0.00379 ( 2) link_BETA1-4 : angle 3.25388 ( 6) link_NAG-ASN : bond 0.00344 ( 6) link_NAG-ASN : angle 2.74616 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 PHE cc_start: 0.8298 (t80) cc_final: 0.8069 (t80) REVERT: B 410 MET cc_start: 0.7891 (ppp) cc_final: 0.7368 (ttt) REVERT: B 583 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8136 (mp) REVERT: B 626 MET cc_start: 0.8332 (tpp) cc_final: 0.7863 (tpp) REVERT: B 725 LYS cc_start: 0.7748 (mttt) cc_final: 0.7532 (mmtt) REVERT: B 789 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7728 (pp) REVERT: B 800 ARG cc_start: 0.8150 (mmm160) cc_final: 0.7671 (tpp80) REVERT: B 862 MET cc_start: 0.8831 (mmt) cc_final: 0.8500 (mpp) REVERT: B 863 LEU cc_start: 0.8983 (tp) cc_final: 0.8682 (tp) REVERT: A 160 PHE cc_start: 0.8308 (t80) cc_final: 0.8082 (t80) REVERT: A 410 MET cc_start: 0.7974 (ppp) cc_final: 0.7575 (ppp) REVERT: A 626 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7843 (tpp) REVERT: A 789 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7803 (pp) REVERT: A 800 ARG cc_start: 0.8182 (mmm160) cc_final: 0.7508 (tpp80) REVERT: A 862 MET cc_start: 0.8844 (mmt) cc_final: 0.8516 (mpp) REVERT: A 863 LEU cc_start: 0.8988 (tp) cc_final: 0.8689 (tp) REVERT: A 907 ILE cc_start: 0.5398 (OUTLIER) cc_final: 0.5191 (mp) REVERT: A 1104 ARG cc_start: 0.8091 (ttm110) cc_final: 0.7857 (mmt-90) outliers start: 40 outliers final: 30 residues processed: 220 average time/residue: 0.1059 time to fit residues: 35.9270 Evaluate side-chains 220 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 TRP Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 872 LYS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 170 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.118299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.096637 restraints weight = 32500.275| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.98 r_work: 0.3389 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 14324 Z= 0.173 Angle : 0.703 11.875 19454 Z= 0.344 Chirality : 0.044 0.228 2248 Planarity : 0.004 0.033 2430 Dihedral : 5.459 38.429 2104 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.53 % Allowed : 16.80 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.19), residues: 1778 helix: 0.22 (0.17), residues: 970 sheet: 0.28 (0.41), residues: 162 loop : -2.69 (0.21), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 348 TYR 0.012 0.001 TYR A 617 PHE 0.030 0.002 PHE B 207 TRP 0.014 0.001 TRP A 811 HIS 0.007 0.001 HIS A1074 Details of bonding type rmsd covalent geometry : bond 0.00416 (14308) covalent geometry : angle 0.69307 (19414) SS BOND : bond 0.00441 ( 8) SS BOND : angle 2.29676 ( 16) hydrogen bonds : bond 0.03753 ( 627) hydrogen bonds : angle 4.24711 ( 1809) link_BETA1-4 : bond 0.00291 ( 2) link_BETA1-4 : angle 3.14765 ( 6) link_NAG-ASN : bond 0.00250 ( 6) link_NAG-ASN : angle 2.85791 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 PHE cc_start: 0.8349 (t80) cc_final: 0.8106 (t80) REVERT: B 583 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8158 (mt) REVERT: B 626 MET cc_start: 0.8346 (tpp) cc_final: 0.7752 (tpp) REVERT: B 646 LEU cc_start: 0.8172 (mt) cc_final: 0.7833 (mt) REVERT: B 725 LYS cc_start: 0.7862 (mttt) cc_final: 0.7636 (mmtt) REVERT: B 789 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7882 (pp) REVERT: B 862 MET cc_start: 0.8939 (mmt) cc_final: 0.8584 (mpp) REVERT: B 863 LEU cc_start: 0.8978 (tp) cc_final: 0.8675 (tp) REVERT: B 864 LEU cc_start: 0.8908 (mm) cc_final: 0.8622 (mm) REVERT: A 160 PHE cc_start: 0.8367 (t80) cc_final: 0.8120 (t80) REVERT: A 410 MET cc_start: 0.7957 (ppp) cc_final: 0.7230 (ttt) REVERT: A 626 MET cc_start: 0.8361 (tpp) cc_final: 0.7758 (tpp) REVERT: A 646 LEU cc_start: 0.8193 (mt) cc_final: 0.7853 (mt) REVERT: A 789 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7914 (pp) REVERT: A 862 MET cc_start: 0.8939 (mmt) cc_final: 0.8614 (mpp) REVERT: A 863 LEU cc_start: 0.8980 (tp) cc_final: 0.8673 (tp) REVERT: A 864 LEU cc_start: 0.8926 (mm) cc_final: 0.8648 (mm) REVERT: A 907 ILE cc_start: 0.5497 (OUTLIER) cc_final: 0.5281 (mp) outliers start: 38 outliers final: 23 residues processed: 216 average time/residue: 0.1030 time to fit residues: 34.1943 Evaluate side-chains 204 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 TRP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 811 TRP Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1121 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 84 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 163 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.118741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097965 restraints weight = 31742.763| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.90 r_work: 0.3411 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14324 Z= 0.131 Angle : 0.666 11.799 19454 Z= 0.324 Chirality : 0.043 0.189 2248 Planarity : 0.003 0.031 2430 Dihedral : 5.379 38.189 2104 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.67 % Allowed : 16.53 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.19), residues: 1778 helix: 0.28 (0.17), residues: 978 sheet: 0.31 (0.41), residues: 162 loop : -2.65 (0.21), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 348 TYR 0.007 0.001 TYR A 617 PHE 0.034 0.001 PHE A 207 TRP 0.013 0.001 TRP B 811 HIS 0.003 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00308 (14308) covalent geometry : angle 0.65697 (19414) SS BOND : bond 0.00384 ( 8) SS BOND : angle 1.97670 ( 16) hydrogen bonds : bond 0.03603 ( 627) hydrogen bonds : angle 4.16931 ( 1809) link_BETA1-4 : bond 0.00286 ( 2) link_BETA1-4 : angle 3.21597 ( 6) link_NAG-ASN : bond 0.00321 ( 6) link_NAG-ASN : angle 2.76196 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2786.40 seconds wall clock time: 48 minutes 38.68 seconds (2918.68 seconds total)