Starting phenix.real_space_refine on Fri Jul 3 11:54:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d8z_30615/07_2026/7d8z_30615.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d8z_30615/07_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_30615/07_2026/7d8z_30615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d8z_30615/07_2026/7d8z_30615.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7d8z_30615/07_2026/7d8z_30615.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d8z_30615/07_2026/7d8z_30615.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d8z_30615/07_2026/7d8z_30615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d8z_30615/07_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-6108/lib/python3.11/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 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 chiralities: 2 Restraints were copied for chains: A, D Time building chain proxies: 7.38, per 1000 atoms: 0.53 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: 1.12 Conformation dependent library (CDL) restraints added in 578.9 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: 0.44 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: 2.57 Time building geometry restraints manager: 1.54 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: 7892 15.43 - 30.86: 378 30.86 - 46.29: 94 46.29 - 61.73: 2 61.73 - 77.16: 8 Dihedral angle restraints: 8374 sinusoidal: 3276 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 8371 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.160 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 10.040 77.158 5090 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/Z covalent geometry : bond 0.00856 / 0.38 (14308) covalent geometry : angle 1.14808 / 0.65 (19414) SS BOND : bond 0.01355 / 0.86 ( 8) SS BOND : angle 2.90720 / 1.83 ( 16) hydrogen bonds : bond 0.30944 / 20.30 ( 627) hydrogen bonds : angle 10.32120 / 7.00 ( 1809) link_BETA1-4 : bond 0.00383 / 0.19 ( 2) link_BETA1-4 : angle 7.51549 / 4.11 ( 6) link_NAG-ASN : bond 0.02438 / 1.39 ( 6) link_NAG-ASN : angle 11.07526 / 6.82 ( 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 : 0.551 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: 0.1501 time to fit residues: 76.7084 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 : 0.541 ------------------------------------------------------------------------------- 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... 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 = 0.118692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097333 restraints weight = 32009.437| |-----------------------------------------------------------------------------| 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: 0.7909 moved from start: 0.2886 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= 0.161 Angle : 0.762 9.309 19454 Z= 0.389 Chirality : 0.046 0.247 2248 Planarity : 0.006 0.051 2430 Dihedral : 5.864 40.744 1936 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 1.67 % Allowed : 10.80 % Favored : 87.53 % 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: -3.78 (0.16), residues: 1778 helix: -2.25 (0.13), residues: 960 sheet: -0.45 (0.39), residues: 154 loop : -3.27 (0.19), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 880 TYR 0.029 0.002 TYR B 414 PHE 0.020 0.002 PHE A 156 TRP 0.016 0.001 TRP B 693 HIS 0.011 0.002 HIS A1074 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (14308) covalent geometry : angle 0.74596 / 0.38 (19414) SS BOND : bond 0.02072 / 1.20 ( 8) SS BOND : angle 3.74061 / 2.03 ( 16) hydrogen bonds : bond 0.05978 / 3.92 ( 627) hydrogen bonds : angle 5.55716 / 3.77 ( 1809) link_BETA1-4 : bond 0.00334 / 0.17 ( 2) link_BETA1-4 : angle 4.12181 / 2.21 ( 6) link_NAG-ASN : bond 0.00294 / 0.14 ( 6) link_NAG-ASN : angle 3.10226 / 1.84 ( 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 : 0.470 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: 0.8231 (t80) cc_final: 0.8004 (t80) REVERT: B 727 LEU cc_start: 0.8634 (tp) cc_final: 0.8091 (tp) REVERT: B 800 ARG cc_start: 0.8061 (mmm160) cc_final: 0.7389 (tpp80) REVERT: B 863 LEU cc_start: 0.9031 (tp) cc_final: 0.8746 (tp) REVERT: B 864 LEU cc_start: 0.8863 (mm) cc_final: 0.8661 (mm) REVERT: B 879 MET cc_start: 0.7990 (ttm) cc_final: 0.7772 (ttm) REVERT: A 160 PHE cc_start: 0.8224 (t80) cc_final: 0.7999 (t80) REVERT: A 727 LEU cc_start: 0.8646 (tp) cc_final: 0.8154 (tp) REVERT: A 800 ARG cc_start: 0.8082 (mmm160) cc_final: 0.7381 (tpp80) REVERT: A 863 LEU cc_start: 0.9029 (tp) cc_final: 0.8733 (tp) REVERT: A 864 LEU cc_start: 0.8854 (mm) cc_final: 0.8651 (mm) REVERT: A 879 MET cc_start: 0.8007 (ttm) cc_final: 0.7780 (ttm) outliers start: 25 outliers final: 15 residues processed: 277 average time/residue: 0.1150 time to fit residues: 47.4113 Evaluate side-chains 209 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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: 0.0670 chunk 62 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 168 optimal weight: 8.9990 chunk 14 optimal weight: 0.0050 chunk 87 optimal weight: 8.9990 chunk 128 optimal weight: 0.4980 chunk 15 optimal weight: 0.3980 overall best weight: 0.3532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 133 ASN B 361 ASN B 494 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.121020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.099401 restraints weight = 31988.589| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.05 r_work: 0.3444 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14324 Z= 0.127 Angle : 0.652 7.819 19454 Z= 0.330 Chirality : 0.044 0.229 2248 Planarity : 0.004 0.039 2430 Dihedral : 5.293 33.524 1936 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.33 % Allowed : 11.93 % Favored : 85.73 % 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: -2.69 (0.18), residues: 1778 helix: -1.11 (0.15), residues: 972 sheet: -0.68 (0.37), residues: 168 loop : -3.09 (0.20), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 880 TYR 0.012 0.001 TYR A 430 PHE 0.026 0.001 PHE B 207 TRP 0.016 0.001 TRP A 693 HIS 0.004 0.001 HIS A 904 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (14308) covalent geometry : angle 0.64344 / 0.33 (19414) SS BOND : bond 0.00341 / 0.19 ( 8) SS BOND : angle 1.92685 / 1.14 ( 16) hydrogen bonds : bond 0.04401 / 2.90 ( 627) hydrogen bonds : angle 4.79155 / 3.26 ( 1809) link_BETA1-4 : bond 0.00312 / 0.15 ( 2) link_BETA1-4 : angle 3.90306 / 2.13 ( 6) link_NAG-ASN : bond 0.00569 / 0.33 ( 6) link_NAG-ASN : angle 2.11968 / 1.17 ( 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 264 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 0.557 Fit side-chains 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 578 ASP cc_start: 0.7177 (p0) cc_final: 0.6953 (p0) REVERT: B 583 ILE cc_start: 0.8626 (mt) cc_final: 0.8353 (mt) REVERT: B 593 MET cc_start: 0.8372 (ttp) cc_final: 0.8144 (tpt) REVERT: B 789 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7668 (pp) REVERT: B 800 ARG cc_start: 0.8079 (mmm160) cc_final: 0.7439 (tpp80) REVERT: B 863 LEU cc_start: 0.9003 (tp) cc_final: 0.8723 (tp) REVERT: B 864 LEU cc_start: 0.8880 (mm) cc_final: 0.8635 (mm) REVERT: B 907 ILE cc_start: 0.5219 (OUTLIER) cc_final: 0.4993 (mp) REVERT: A 160 PHE cc_start: 0.8235 (t80) cc_final: 0.7983 (t80) REVERT: A 578 ASP cc_start: 0.7210 (p0) cc_final: 0.6989 (p0) REVERT: A 583 ILE cc_start: 0.8623 (mt) cc_final: 0.8352 (mt) REVERT: A 593 MET cc_start: 0.8385 (ttp) cc_final: 0.8148 (tpt) REVERT: A 727 LEU cc_start: 0.8627 (tp) cc_final: 0.8353 (tp) REVERT: A 789 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7583 (pp) REVERT: A 800 ARG cc_start: 0.8092 (mmm160) cc_final: 0.7431 (tpp80) REVERT: A 863 LEU cc_start: 0.8998 (tp) cc_final: 0.8719 (tp) REVERT: A 864 LEU cc_start: 0.8886 (mm) cc_final: 0.8643 (mm) REVERT: A 907 ILE cc_start: 0.5225 (OUTLIER) cc_final: 0.5000 (mp) outliers start: 35 outliers final: 17 residues processed: 250 average time/residue: 0.1116 time to fit residues: 42.1967 Evaluate side-chains 225 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 700 LEU Chi-restraints excluded: chain B residue 789 LEU 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 700 LEU Chi-restraints excluded: chain A residue 789 LEU 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: 0.0170 chunk 21 optimal weight: 0.0670 chunk 164 optimal weight: 0.4980 chunk 79 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 15 optimal weight: 0.0030 chunk 133 optimal weight: 1.9990 overall best weight: 0.2766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 252 ASN ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 HIS A 252 ASN ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.121518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.100398 restraints weight = 31801.408| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.98 r_work: 0.3459 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14324 Z= 0.119 Angle : 0.625 7.830 19454 Z= 0.312 Chirality : 0.043 0.202 2248 Planarity : 0.003 0.038 2430 Dihedral : 5.059 30.119 1936 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.60 % Allowed : 12.47 % Favored : 83.93 % 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: -0.63 (0.16), residues: 968 sheet: -0.45 (0.37), residues: 164 loop : -3.04 (0.20), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 348 TYR 0.008 0.001 TYR A 639 PHE 0.029 0.001 PHE B 207 TRP 0.012 0.001 TRP A 693 HIS 0.004 0.001 HIS A1074 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (14308) covalent geometry : angle 0.61779 / 0.31 (19414) SS BOND : bond 0.00168 / 0.08 ( 8) SS BOND : angle 1.45492 / 0.93 ( 16) hydrogen bonds : bond 0.03823 / 2.51 ( 627) hydrogen bonds : angle 4.53803 / 3.09 ( 1809) link_BETA1-4 : bond 0.00665 / 0.34 ( 2) link_BETA1-4 : angle 3.45635 / 1.87 ( 6) link_NAG-ASN : bond 0.00333 / 0.15 ( 6) link_NAG-ASN : angle 2.21853 / 1.28 ( 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 283 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 229 time to evaluate : 0.617 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: 0.8238 (t80) cc_final: 0.7986 (t80) REVERT: B 583 ILE cc_start: 0.8613 (mt) cc_final: 0.8365 (mt) REVERT: B 727 LEU cc_start: 0.8632 (tp) cc_final: 0.8398 (tp) REVERT: B 789 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7617 (pp) REVERT: B 800 ARG cc_start: 0.7977 (mmm160) cc_final: 0.7457 (tpp80) REVERT: B 863 LEU cc_start: 0.9018 (tp) cc_final: 0.8707 (tp) REVERT: B 864 LEU cc_start: 0.8919 (mm) cc_final: 0.8589 (mm) REVERT: B 907 ILE cc_start: 0.5180 (OUTLIER) cc_final: 0.4858 (mp) REVERT: A 160 PHE cc_start: 0.8235 (t80) cc_final: 0.7983 (t80) REVERT: A 583 ILE cc_start: 0.8604 (mt) cc_final: 0.8357 (mt) REVERT: A 727 LEU cc_start: 0.8605 (tp) cc_final: 0.8399 (tp) REVERT: A 789 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7610 (pp) REVERT: A 863 LEU cc_start: 0.9021 (tp) cc_final: 0.8714 (tp) REVERT: A 864 LEU cc_start: 0.8925 (mm) cc_final: 0.8586 (mm) REVERT: A 907 ILE cc_start: 0.5192 (OUTLIER) cc_final: 0.4860 (mp) outliers start: 54 outliers final: 29 residues processed: 260 average time/residue: 0.1089 time to fit residues: 43.0612 Evaluate side-chains 232 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 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 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 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 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 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 907 ILE 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: 5.9990 chunk 25 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 15 optimal weight: 0.0470 chunk 167 optimal weight: 4.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3848 r_free = 0.3848 target = 0.119043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.098499 restraints weight = 32059.040| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.92 r_work: 0.3430 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14324 Z= 0.134 Angle : 0.628 7.667 19454 Z= 0.312 Chirality : 0.043 0.204 2248 Planarity : 0.003 0.038 2430 Dihedral : 4.953 31.847 1936 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.00 % Allowed : 13.93 % Favored : 82.07 % 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: -1.95 (0.18), residues: 1778 helix: -0.42 (0.16), residues: 984 sheet: -0.31 (0.38), residues: 164 loop : -2.94 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1104 TYR 0.009 0.001 TYR A 430 PHE 0.020 0.001 PHE B 207 TRP 0.014 0.001 TRP B 798 HIS 0.003 0.001 HIS A1074 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (14308) covalent geometry : angle 0.62097 / 0.31 (19414) SS BOND : bond 0.00203 / 0.10 ( 8) SS BOND : angle 1.80693 / 1.16 ( 16) hydrogen bonds : bond 0.03848 / 2.52 ( 627) hydrogen bonds : angle 4.47765 / 3.05 ( 1809) link_BETA1-4 : bond 0.00713 / 0.36 ( 2) link_BETA1-4 : angle 3.16791 / 1.71 ( 6) link_NAG-ASN : bond 0.00400 / 0.19 ( 6) link_NAG-ASN : angle 2.11747 / 1.15 ( 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 273 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 213 time to evaluate : 0.402 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 160 PHE cc_start: 0.8260 (t80) cc_final: 0.8005 (t80) REVERT: B 583 ILE cc_start: 0.8619 (mt) cc_final: 0.8354 (mt) REVERT: B 594 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8229 (m-80) REVERT: B 727 LEU cc_start: 0.8719 (tp) cc_final: 0.8489 (tp) REVERT: B 789 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7628 (pp) REVERT: B 863 LEU cc_start: 0.9023 (tp) cc_final: 0.8742 (tp) REVERT: B 907 ILE cc_start: 0.5310 (OUTLIER) cc_final: 0.4990 (mp) REVERT: B 1104 ARG cc_start: 0.8062 (ttm-80) cc_final: 0.7749 (mmp80) REVERT: A 160 PHE cc_start: 0.8265 (t80) cc_final: 0.8011 (t80) REVERT: A 583 ILE cc_start: 0.8611 (mt) cc_final: 0.8347 (mt) REVERT: A 594 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.8243 (m-80) REVERT: A 721 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8484 (tt) REVERT: A 727 LEU cc_start: 0.8760 (tp) cc_final: 0.8556 (tp) REVERT: A 789 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7618 (pp) REVERT: A 863 LEU cc_start: 0.9025 (tp) cc_final: 0.8734 (tp) REVERT: A 907 ILE cc_start: 0.5326 (OUTLIER) cc_final: 0.4998 (mp) outliers start: 60 outliers final: 43 residues processed: 243 average time/residue: 0.1119 time to fit residues: 40.7608 Evaluate side-chains 249 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 585 SER Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 594 PHE 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 722 LYS 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 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 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 585 SER Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 594 PHE 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 721 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 1121 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 13 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 9 optimal weight: 0.0000 chunk 106 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 HIS B1096 ASN ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.120399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.098987 restraints weight = 32087.241| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.98 r_work: 0.3439 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4170 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= 0.118 Angle : 0.613 7.724 19454 Z= 0.306 Chirality : 0.043 0.222 2248 Planarity : 0.003 0.037 2430 Dihedral : 4.838 31.107 1936 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.33 % Allowed : 14.80 % Favored : 81.87 % 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: -1.56 (0.19), residues: 1778 helix: -0.06 (0.16), residues: 974 sheet: 0.04 (0.39), residues: 160 loop : -2.85 (0.21), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1104 TYR 0.010 0.001 TYR A 294 PHE 0.034 0.001 PHE B 207 TRP 0.012 0.001 TRP B 811 HIS 0.002 0.001 HIS B 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (14308) covalent geometry : angle 0.60674 / 0.30 (19414) SS BOND : bond 0.00239 / 0.12 ( 8) SS BOND : angle 1.73818 / 1.11 ( 16) hydrogen bonds : bond 0.03635 / 2.38 ( 627) hydrogen bonds : angle 4.31881 / 2.94 ( 1809) link_BETA1-4 : bond 0.00483 / 0.25 ( 2) link_BETA1-4 : angle 3.05383 / 1.66 ( 6) link_NAG-ASN : bond 0.00340 / 0.17 ( 6) link_NAG-ASN : angle 1.98081 / 1.08 ( 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 261 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 211 time to evaluate : 0.532 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: 0.8226 (t80) cc_final: 0.7980 (t80) REVERT: B 583 ILE cc_start: 0.8593 (mt) cc_final: 0.8341 (mt) REVERT: B 594 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8194 (m-80) REVERT: B 789 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7551 (pp) REVERT: B 800 ARG cc_start: 0.8180 (mmm160) cc_final: 0.7472 (tpp80) REVERT: B 862 MET cc_start: 0.8838 (mmt) cc_final: 0.8540 (mpp) REVERT: B 863 LEU cc_start: 0.9006 (tp) cc_final: 0.8713 (tp) REVERT: A 160 PHE cc_start: 0.8230 (t80) cc_final: 0.7982 (t80) REVERT: A 583 ILE cc_start: 0.8570 (mt) cc_final: 0.8321 (mt) REVERT: A 594 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8258 (m-80) REVERT: A 626 MET cc_start: 0.8180 (tpp) cc_final: 0.7910 (tpp) REVERT: A 721 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8473 (tt) REVERT: A 789 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7499 (pp) REVERT: A 800 ARG cc_start: 0.8089 (mmm160) cc_final: 0.7621 (tpp80) REVERT: A 862 MET cc_start: 0.8826 (mmm) cc_final: 0.8566 (mpp) REVERT: A 863 LEU cc_start: 0.9024 (tp) cc_final: 0.8754 (tp) outliers start: 50 outliers final: 39 residues processed: 240 average time/residue: 0.1041 time to fit residues: 38.4675 Evaluate side-chains 241 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 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 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 577 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 594 PHE 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 789 LEU Chi-restraints excluded: chain B residue 811 TRP Chi-restraints excluded: chain B residue 840 ASN 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 166 THR 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 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 590 MET Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 721 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 1121 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 59 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 chunk 88 optimal weight: 0.5980 chunk 74 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 chunk 135 optimal weight: 0.2980 chunk 130 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3841 r_free = 0.3841 target = 0.118748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.097886 restraints weight = 31915.001| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.97 r_work: 0.3413 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4207 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= 0.145 Angle : 0.649 12.292 19454 Z= 0.320 Chirality : 0.044 0.266 2248 Planarity : 0.003 0.037 2430 Dihedral : 4.862 32.421 1936 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.60 % Allowed : 15.20 % Favored : 81.20 % 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: -1.39 (0.19), residues: 1778 helix: 0.11 (0.17), residues: 976 sheet: -0.04 (0.39), residues: 164 loop : -2.83 (0.21), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 348 TYR 0.010 0.001 TYR B 617 PHE 0.032 0.002 PHE B 207 TRP 0.012 0.001 TRP B 811 HIS 0.002 0.001 HIS B 711 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (14308) covalent geometry : angle 0.64231 / 0.32 (19414) SS BOND : bond 0.00283 / 0.14 ( 8) SS BOND : angle 1.83286 / 1.16 ( 16) hydrogen bonds : bond 0.03729 / 2.44 ( 627) hydrogen bonds : angle 4.32209 / 2.96 ( 1809) link_BETA1-4 : bond 0.00479 / 0.24 ( 2) link_BETA1-4 : angle 2.81867 / 1.53 ( 6) link_NAG-ASN : bond 0.00271 / 0.13 ( 6) link_NAG-ASN : angle 2.09121 / 1.22 ( 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 256 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 202 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: 0.8286 (t80) cc_final: 0.8043 (t80) REVERT: B 410 MET cc_start: 0.7924 (ppp) cc_final: 0.7282 (ttt) REVERT: B 583 ILE cc_start: 0.8565 (mt) cc_final: 0.8315 (mt) REVERT: B 594 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.8295 (m-80) REVERT: B 725 LYS cc_start: 0.7764 (mttt) cc_final: 0.7554 (mmtt) REVERT: B 789 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7662 (pp) REVERT: B 863 LEU cc_start: 0.9016 (tp) cc_final: 0.8737 (tp) REVERT: A 160 PHE cc_start: 0.8288 (t80) cc_final: 0.8049 (t80) REVERT: A 583 ILE cc_start: 0.8577 (mt) cc_final: 0.8328 (mt) REVERT: A 594 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8297 (m-80) REVERT: A 721 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8515 (tt) REVERT: A 789 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7678 (pp) REVERT: A 862 MET cc_start: 0.8878 (mmm) cc_final: 0.8613 (mpp) REVERT: A 863 LEU cc_start: 0.9028 (tp) cc_final: 0.8757 (tp) outliers start: 54 outliers final: 43 residues processed: 238 average time/residue: 0.1053 time to fit residues: 38.6740 Evaluate side-chains 242 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 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 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 577 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 594 PHE 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 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 1121 LEU 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 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 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 577 LEU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 721 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 1121 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 47 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 167 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 73 optimal weight: 9.9990 chunk 18 optimal weight: 0.0070 chunk 109 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 overall best weight: 2.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3830 r_free = 0.3830 target = 0.118198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.097128 restraints weight = 31754.818| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.96 r_work: 0.3401 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 14324 Z= 0.165 Angle : 0.673 9.410 19454 Z= 0.335 Chirality : 0.044 0.234 2248 Planarity : 0.003 0.037 2430 Dihedral : 4.913 32.555 1936 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.93 % Allowed : 14.67 % Favored : 81.40 % 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: -1.35 (0.19), residues: 1778 helix: 0.15 (0.17), residues: 970 sheet: 0.08 (0.40), residues: 162 loop : -2.81 (0.20), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 348 TYR 0.011 0.001 TYR B 617 PHE 0.034 0.002 PHE B 207 TRP 0.013 0.001 TRP A 811 HIS 0.003 0.001 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (14308) covalent geometry : angle 0.66732 / 0.33 (19414) SS BOND : bond 0.00312 / 0.16 ( 8) SS BOND : angle 1.90262 / 1.21 ( 16) hydrogen bonds : bond 0.03838 / 2.51 ( 627) hydrogen bonds : angle 4.33668 / 2.97 ( 1809) link_BETA1-4 : bond 0.00464 / 0.23 ( 2) link_BETA1-4 : angle 2.74922 / 1.48 ( 6) link_NAG-ASN : bond 0.00319 / 0.18 ( 6) link_NAG-ASN : angle 1.99642 / 1.13 ( 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 248 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 189 time to evaluate : 0.557 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: 0.8277 (t80) cc_final: 0.8034 (t80) REVERT: B 410 MET cc_start: 0.7943 (ppp) cc_final: 0.7402 (ttt) REVERT: B 583 ILE cc_start: 0.8617 (mt) cc_final: 0.8372 (mt) REVERT: B 590 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8100 (tpt) REVERT: B 594 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.8262 (m-80) REVERT: B 789 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7792 (pp) REVERT: B 862 MET cc_start: 0.8870 (mmt) cc_final: 0.8600 (mpp) REVERT: B 863 LEU cc_start: 0.9023 (tp) cc_final: 0.8712 (tp) REVERT: A 160 PHE cc_start: 0.8286 (t80) cc_final: 0.8046 (t80) REVERT: A 583 ILE cc_start: 0.8609 (mt) cc_final: 0.8364 (mt) REVERT: A 590 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.8010 (tpt) REVERT: A 594 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: A 626 MET cc_start: 0.8519 (tpp) cc_final: 0.8222 (tpp) REVERT: A 721 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8503 (tt) REVERT: A 789 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7819 (pp) REVERT: A 862 MET cc_start: 0.8848 (mmm) cc_final: 0.8593 (mpp) REVERT: A 863 LEU cc_start: 0.9015 (tp) cc_final: 0.8748 (tp) outliers start: 59 outliers final: 40 residues processed: 231 average time/residue: 0.1130 time to fit residues: 39.5069 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 : 0.524 ------------------------------------------------------------------------------- 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 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 474 VAL Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 594 PHE 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 789 LEU Chi-restraints excluded: chain B residue 811 TRP Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 840 ASN 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 166 THR 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 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 577 LEU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 594 PHE 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 721 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 1121 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 20 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 0.0870 chunk 147 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 162 optimal weight: 6.9990 chunk 163 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3840 r_free = 0.3840 target = 0.118915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.098422 restraints weight = 31581.363| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.88 r_work: 0.3422 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4453 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= 0.128 Angle : 0.658 15.058 19454 Z= 0.322 Chirality : 0.043 0.252 2248 Planarity : 0.003 0.039 2430 Dihedral : 4.860 31.639 1936 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.47 % Allowed : 15.20 % Favored : 81.33 % 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: -1.23 (0.19), residues: 1778 helix: 0.22 (0.17), residues: 978 sheet: 0.13 (0.40), residues: 162 loop : -2.73 (0.21), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 348 TYR 0.007 0.001 TYR A 430 PHE 0.038 0.001 PHE B 207 TRP 0.015 0.001 TRP A 811 HIS 0.004 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (14308) covalent geometry : angle 0.65235 / 0.32 (19414) SS BOND : bond 0.00232 / 0.13 ( 8) SS BOND : angle 1.66632 / 1.06 ( 16) hydrogen bonds : bond 0.03692 / 2.40 ( 627) hydrogen bonds : angle 4.26045 / 2.92 ( 1809) link_BETA1-4 : bond 0.00502 / 0.25 ( 2) link_BETA1-4 : angle 2.72713 / 1.48 ( 6) link_NAG-ASN : bond 0.00368 / 0.20 ( 6) link_NAG-ASN : angle 1.81724 / 1.03 ( 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 249 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 197 time to evaluate : 0.469 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 160 PHE cc_start: 0.8264 (t80) cc_final: 0.8032 (t80) REVERT: B 583 ILE cc_start: 0.8555 (mt) cc_final: 0.8325 (mt) REVERT: B 594 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.8117 (m-80) REVERT: B 725 LYS cc_start: 0.7794 (mttt) cc_final: 0.7574 (mmtt) REVERT: B 789 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7833 (pp) REVERT: B 800 ARG cc_start: 0.8143 (mmm160) cc_final: 0.7643 (tpp80) REVERT: B 862 MET cc_start: 0.8865 (mmt) cc_final: 0.8582 (mpp) REVERT: B 863 LEU cc_start: 0.8989 (tp) cc_final: 0.8686 (tp) REVERT: B 864 LEU cc_start: 0.8907 (mm) cc_final: 0.8645 (mm) REVERT: A 160 PHE cc_start: 0.8296 (t80) cc_final: 0.8066 (t80) REVERT: A 410 MET cc_start: 0.7965 (ppp) cc_final: 0.7513 (ppp) REVERT: A 583 ILE cc_start: 0.8545 (mt) cc_final: 0.8315 (mt) REVERT: A 594 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8168 (m-80) REVERT: A 626 MET cc_start: 0.8486 (tpp) cc_final: 0.8229 (tpp) REVERT: A 721 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8411 (tt) REVERT: A 789 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7860 (pp) REVERT: A 862 MET cc_start: 0.8864 (mmm) cc_final: 0.8578 (mpp) REVERT: A 863 LEU cc_start: 0.9008 (tp) cc_final: 0.8740 (tp) outliers start: 52 outliers final: 39 residues processed: 233 average time/residue: 0.0929 time to fit residues: 33.6451 Evaluate side-chains 230 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 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 577 LEU Chi-restraints excluded: chain B residue 594 PHE 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 789 LEU Chi-restraints excluded: chain B residue 811 TRP Chi-restraints excluded: chain B residue 834 VAL 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 164 SER 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 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 573 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 721 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 1121 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 170 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3810 r_free = 0.3810 target = 0.116991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.095639 restraints weight = 32405.760| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.01 r_work: 0.3376 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 14324 Z= 0.197 Angle : 0.734 12.862 19454 Z= 0.361 Chirality : 0.046 0.244 2248 Planarity : 0.004 0.037 2430 Dihedral : 5.022 36.623 1936 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.47 % Allowed : 15.87 % 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: -1.38 (0.19), residues: 1778 helix: 0.04 (0.16), residues: 982 sheet: 0.18 (0.41), residues: 162 loop : -2.77 (0.21), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 348 TYR 0.012 0.001 TYR B 617 PHE 0.036 0.002 PHE B 207 TRP 0.013 0.001 TRP A 811 HIS 0.004 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (14308) covalent geometry : angle 0.72719 / 0.36 (19414) SS BOND : bond 0.00218 / 0.11 ( 8) SS BOND : angle 2.39679 / 1.50 ( 16) hydrogen bonds : bond 0.04058 / 2.63 ( 627) hydrogen bonds : angle 4.47756 / 3.07 ( 1809) link_BETA1-4 : bond 0.00531 / 0.27 ( 2) link_BETA1-4 : angle 2.58108 / 1.39 ( 6) link_NAG-ASN : bond 0.00296 / 0.17 ( 6) link_NAG-ASN : angle 1.96986 / 1.09 ( 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 231 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 179 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 PHE cc_start: 0.8310 (t80) cc_final: 0.8062 (t80) REVERT: B 583 ILE cc_start: 0.8554 (mt) cc_final: 0.8338 (mt) REVERT: B 594 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8257 (m-80) REVERT: B 789 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7895 (pp) REVERT: B 800 ARG cc_start: 0.8168 (mmm160) cc_final: 0.7431 (tpp80) REVERT: B 837 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7405 (t80) REVERT: B 862 MET cc_start: 0.8962 (mmt) cc_final: 0.8655 (mpp) REVERT: B 863 LEU cc_start: 0.8988 (tp) cc_final: 0.8689 (tp) REVERT: B 864 LEU cc_start: 0.8896 (mm) cc_final: 0.8633 (mm) REVERT: A 160 PHE cc_start: 0.8325 (t80) cc_final: 0.8077 (t80) REVERT: A 410 MET cc_start: 0.7992 (ppp) cc_final: 0.7567 (ppp) REVERT: A 583 ILE cc_start: 0.8585 (mt) cc_final: 0.8371 (mt) REVERT: A 594 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8243 (m-80) REVERT: A 626 MET cc_start: 0.8497 (tpp) cc_final: 0.8154 (tpp) REVERT: A 721 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8536 (tt) REVERT: A 789 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7948 (pp) REVERT: A 837 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7444 (t80) REVERT: A 862 MET cc_start: 0.8896 (mmm) cc_final: 0.8609 (mpp) REVERT: A 863 LEU cc_start: 0.8992 (tp) cc_final: 0.8699 (tp) REVERT: A 864 LEU cc_start: 0.8944 (mm) cc_final: 0.8651 (mm) outliers start: 52 outliers final: 35 residues processed: 218 average time/residue: 0.0993 time to fit residues: 33.4512 Evaluate side-chains 220 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 164 SER 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 573 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 811 TRP Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 837 PHE 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 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 468 VAL Chi-restraints excluded: chain A residue 474 VAL 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 594 PHE Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 721 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 872 LYS 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: 4.9990 chunk 87 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3841 r_free = 0.3841 target = 0.119080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.098406 restraints weight = 31540.037| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.89 r_work: 0.3429 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4621 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= 0.127 Angle : 0.670 11.976 19454 Z= 0.328 Chirality : 0.044 0.266 2248 Planarity : 0.003 0.040 2430 Dihedral : 4.883 35.548 1936 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.60 % Allowed : 16.20 % Favored : 81.20 % 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: -1.15 (0.19), residues: 1778 helix: 0.25 (0.17), residues: 978 sheet: 0.20 (0.41), residues: 162 loop : -2.65 (0.21), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 348 TYR 0.008 0.001 TYR B1110 PHE 0.038 0.001 PHE B 207 TRP 0.015 0.001 TRP A 811 HIS 0.002 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (14308) covalent geometry : angle 0.66492 / 0.33 (19414) SS BOND : bond 0.00313 / 0.19 ( 8) SS BOND : angle 1.98766 / 1.27 ( 16) hydrogen bonds : bond 0.03695 / 2.40 ( 627) hydrogen bonds : angle 4.26674 / 2.92 ( 1809) link_BETA1-4 : bond 0.00625 / 0.30 ( 2) link_BETA1-4 : angle 2.64146 / 1.44 ( 6) link_NAG-ASN : bond 0.00411 / 0.22 ( 6) link_NAG-ASN : angle 1.71048 / 0.98 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2929.83 seconds wall clock time: 51 minutes 14.77 seconds (3074.77 seconds total)