Starting phenix.real_space_refine on Sun Jul 5 08:07:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hae_34586/07_2026/8hae_34586.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hae_34586/07_2026/8hae_34586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hae_34586/07_2026/8hae_34586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hae_34586/07_2026/8hae_34586.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hae_34586/07_2026/8hae_34586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hae_34586/07_2026/8hae_34586.map" } resolution = 4.55 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= 1.000 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: 5 Type Number sf(0) Gaussians S 98 5.16 5 C 8498 2.51 5 N 2322 2.21 5 O 2508 1.98 5 H 13272 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26698 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 13349 Classifications: {'peptide': 845} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 39, 'TRANS': 805} Chain breaks: 1 Chain: "B" Number of atoms: 13349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 13349 Classifications: {'peptide': 845} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 39, 'TRANS': 805} Chain breaks: 1 Time building chain proxies: 4.76, per 1000 atoms: 0.18 Number of scatterers: 26698 At special positions: 0 Unit cell: (164.813, 133.052, 83.2648, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 O 2508 8.00 N 2322 7.00 C 8498 6.00 H 13272 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 868.9 milliseconds 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 10 sheets defined 64.9% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 1 through 4 removed outlier: 3.945A pdb=" N ALA A 4 " --> pdb=" O MET A 1 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1 through 4' Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 26 through 40 Proline residue: A 36 - end of helix Processing helix chain 'A' and resid 67 through 76 removed outlier: 3.844A pdb=" N ALA A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN A 74 " --> pdb=" O HIS A 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N CYS A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 110 through 118 removed outlier: 3.590A pdb=" N MET A 114 " --> pdb=" O GLN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 142 removed outlier: 3.693A pdb=" N ASN A 141 " --> pdb=" O TRP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 149 Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 166 through 175 removed outlier: 3.933A pdb=" N CYS A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 173 " --> pdb=" O HIS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.811A pdb=" N GLN A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 208 removed outlier: 3.505A pdb=" N PHE A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 206 " --> pdb=" O TYR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 removed outlier: 3.541A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 removed outlier: 3.622A pdb=" N CYS A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 252 removed outlier: 3.679A pdb=" N TYR A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 265 removed outlier: 3.654A pdb=" N ILE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 282 removed outlier: 4.396A pdb=" N LEU A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 308 Processing helix chain 'A' and resid 314 through 334 removed outlier: 3.534A pdb=" N ILE A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 381 Proline residue: A 359 - end of helix removed outlier: 4.222A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 462 removed outlier: 3.771A pdb=" N VAL A 455 " --> pdb=" O ARG A 451 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR A 460 " --> pdb=" O ILE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 492 removed outlier: 3.867A pdb=" N ILE A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU A 485 " --> pdb=" O CYS A 481 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 508 removed outlier: 3.752A pdb=" N GLU A 507 " --> pdb=" O HIS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 522 removed outlier: 4.373A pdb=" N ARG A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N HIS A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 519 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 526 removed outlier: 3.645A pdb=" N ASP A 526 " --> pdb=" O PRO A 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 523 through 526' Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 561 through 571 removed outlier: 3.764A pdb=" N CYS A 567 " --> pdb=" O PHE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 593 through 608 removed outlier: 3.742A pdb=" N ASN A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 635 removed outlier: 4.247A pdb=" N TYR A 632 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 634 " --> pdb=" O SER A 631 " (cutoff:3.500A) Proline residue: A 635 - end of helix Processing helix chain 'A' and resid 636 through 654 removed outlier: 3.643A pdb=" N ASN A 653 " --> pdb=" O GLY A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 672 removed outlier: 3.809A pdb=" N TYR A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 683 Processing helix chain 'A' and resid 684 through 697 removed outlier: 3.945A pdb=" N ASN A 690 " --> pdb=" O GLU A 686 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN A 697 " --> pdb=" O TRP A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 703 removed outlier: 4.425A pdb=" N GLY A 703 " --> pdb=" O ILE A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 730 removed outlier: 3.749A pdb=" N ILE A 730 " --> pdb=" O GLY A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 735 No H-bonds generated for 'chain 'A' and resid 733 through 735' Processing helix chain 'A' and resid 736 through 750 removed outlier: 4.322A pdb=" N VAL A 741 " --> pdb=" O LYS A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 765 removed outlier: 3.789A pdb=" N GLN A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 758 " --> pdb=" O GLN A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 776 removed outlier: 4.171A pdb=" N LEU A 775 " --> pdb=" O LEU A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 782 removed outlier: 4.153A pdb=" N GLU A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 792 through 799 Processing helix chain 'A' and resid 810 through 821 Processing helix chain 'A' and resid 824 through 837 removed outlier: 4.544A pdb=" N LEU A 830 " --> pdb=" O GLU A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 849 Processing helix chain 'A' and resid 887 through 901 removed outlier: 4.526A pdb=" N LEU A 896 " --> pdb=" O LYS A 892 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N CYS A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 4 removed outlier: 3.944A pdb=" N ALA B 4 " --> pdb=" O MET B 1 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1 through 4' Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 26 through 40 Proline residue: B 36 - end of helix Processing helix chain 'B' and resid 67 through 76 removed outlier: 3.844A pdb=" N ALA B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN B 74 " --> pdb=" O HIS B 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N CYS B 75 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 110 through 118 removed outlier: 3.589A pdb=" N MET B 114 " --> pdb=" O GLN B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 142 removed outlier: 3.693A pdb=" N ASN B 141 " --> pdb=" O TRP B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 149 Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 166 through 175 removed outlier: 3.933A pdb=" N CYS B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 173 " --> pdb=" O HIS B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.812A pdb=" N GLN B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 183 " --> pdb=" O THR B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 208 removed outlier: 3.506A pdb=" N PHE B 203 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 204 " --> pdb=" O PRO B 200 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B 206 " --> pdb=" O TYR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 220 removed outlier: 3.541A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 removed outlier: 3.623A pdb=" N CYS B 236 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 252 removed outlier: 3.680A pdb=" N TYR B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 265 removed outlier: 3.653A pdb=" N ILE B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN B 265 " --> pdb=" O GLN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 282 removed outlier: 4.396A pdb=" N LEU B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 308 Processing helix chain 'B' and resid 314 through 334 removed outlier: 3.534A pdb=" N ILE B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 381 Proline residue: B 359 - end of helix removed outlier: 4.222A pdb=" N LEU B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 376 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 462 removed outlier: 3.770A pdb=" N VAL B 455 " --> pdb=" O ARG B 451 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR B 460 " --> pdb=" O ILE B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 492 removed outlier: 3.867A pdb=" N ILE B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS B 482 " --> pdb=" O GLU B 478 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU B 485 " --> pdb=" O CYS B 481 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 508 removed outlier: 3.753A pdb=" N GLU B 507 " --> pdb=" O HIS B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 522 removed outlier: 4.371A pdb=" N ARG B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N HIS B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE B 518 " --> pdb=" O ARG B 514 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE B 519 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 526 removed outlier: 3.645A pdb=" N ASP B 526 " --> pdb=" O PRO B 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 523 through 526' Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 532 through 537 Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 558 through 560 No H-bonds generated for 'chain 'B' and resid 558 through 560' Processing helix chain 'B' and resid 561 through 571 removed outlier: 3.764A pdb=" N CYS B 567 " --> pdb=" O PHE B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 579 Processing helix chain 'B' and resid 593 through 608 removed outlier: 3.742A pdb=" N ASN B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 635 removed outlier: 4.247A pdb=" N TYR B 632 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN B 634 " --> pdb=" O SER B 631 " (cutoff:3.500A) Proline residue: B 635 - end of helix Processing helix chain 'B' and resid 636 through 654 removed outlier: 3.642A pdb=" N ASN B 653 " --> pdb=" O GLY B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 672 removed outlier: 3.809A pdb=" N TYR B 667 " --> pdb=" O THR B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 683 Processing helix chain 'B' and resid 684 through 697 removed outlier: 3.945A pdb=" N ASN B 690 " --> pdb=" O GLU B 686 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 697 " --> pdb=" O TRP B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 703 removed outlier: 4.425A pdb=" N GLY B 703 " --> pdb=" O ILE B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 730 removed outlier: 3.751A pdb=" N ILE B 730 " --> pdb=" O GLY B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 735 No H-bonds generated for 'chain 'B' and resid 733 through 735' Processing helix chain 'B' and resid 736 through 750 removed outlier: 4.321A pdb=" N VAL B 741 " --> pdb=" O LYS B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 765 removed outlier: 3.790A pdb=" N GLN B 756 " --> pdb=" O ALA B 752 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN B 758 " --> pdb=" O GLN B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 776 removed outlier: 4.171A pdb=" N LEU B 775 " --> pdb=" O LEU B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 782 removed outlier: 4.153A pdb=" N GLU B 782 " --> pdb=" O GLU B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 787 Processing helix chain 'B' and resid 792 through 799 Processing helix chain 'B' and resid 810 through 821 Processing helix chain 'B' and resid 824 through 837 removed outlier: 4.544A pdb=" N LEU B 830 " --> pdb=" O GLU B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 849 Processing helix chain 'B' and resid 887 through 901 removed outlier: 4.526A pdb=" N LEU B 896 " --> pdb=" O LYS B 892 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 897 " --> pdb=" O ASP B 893 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N CYS B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 336 through 337 removed outlier: 4.723A pdb=" N GLY A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 554 through 557 Processing sheet with id=AA3, first strand: chain 'A' and resid 616 through 617 Processing sheet with id=AA4, first strand: chain 'A' and resid 709 through 713 Processing sheet with id=AA5, first strand: chain 'A' and resid 801 through 803 removed outlier: 6.768A pdb=" N GLU A 801 " --> pdb=" O ILE A 860 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ALA A 862 " --> pdb=" O GLU A 801 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR A 803 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 336 through 337 removed outlier: 4.722A pdb=" N GLY B 341 " --> pdb=" O SER B 337 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 554 through 557 Processing sheet with id=AA8, first strand: chain 'B' and resid 616 through 617 Processing sheet with id=AA9, first strand: chain 'B' and resid 709 through 713 Processing sheet with id=AB1, first strand: chain 'B' and resid 801 through 803 removed outlier: 6.768A pdb=" N GLU B 801 " --> pdb=" O ILE B 860 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ALA B 862 " --> pdb=" O GLU B 801 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR B 803 " --> pdb=" O ALA B 862 " (cutoff:3.500A) 602 hydrogen bonds defined for protein. 1728 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: 5.81 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 13228 1.03 - 1.22: 48 1.22 - 1.42: 5747 1.42 - 1.62: 7815 1.62 - 1.82: 152 Bond restraints: 26990 Sorted by residual: bond pdb=" CA VAL A 741 " pdb=" HA VAL A 741 " ideal model delta sigma weight residual 0.970 0.914 0.056 2.00e-02 2.50e+03 7.98e+00 bond pdb=" CD LYS A 798 " pdb=" CE LYS A 798 " ideal model delta sigma weight residual 1.520 1.596 -0.076 3.00e-02 1.11e+03 6.40e+00 bond pdb=" CD LYS B 798 " pdb=" CE LYS B 798 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.22e+00 bond pdb=" CG2 THR B 707 " pdb="HG22 THR B 707 " ideal model delta sigma weight residual 0.970 1.016 -0.046 2.00e-02 2.50e+03 5.22e+00 bond pdb=" CD ARG B 44 " pdb=" NE ARG B 44 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.40e-02 5.10e+03 4.66e+00 ... (remaining 26985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.68: 48666 8.68 - 17.35: 6 17.35 - 26.03: 3 26.03 - 34.71: 38 34.71 - 43.38: 39 Bond angle restraints: 48752 Sorted by residual: angle pdb=" N VAL A 741 " pdb=" CA VAL A 741 " pdb=" HA VAL A 741 " ideal model delta sigma weight residual 110.00 66.62 43.38 3.00e+00 1.11e-01 2.09e+02 angle pdb=" C GLU A 25 " pdb=" CA GLU A 25 " pdb=" HA GLU A 25 " ideal model delta sigma weight residual 109.00 66.02 42.98 3.00e+00 1.11e-01 2.05e+02 angle pdb=" C LEU A 869 " pdb=" CA LEU A 869 " pdb=" HA LEU A 869 " ideal model delta sigma weight residual 109.00 68.22 40.78 3.00e+00 1.11e-01 1.85e+02 angle pdb=" C PHE A 708 " pdb=" CA PHE A 708 " pdb=" HA PHE A 708 " ideal model delta sigma weight residual 109.00 68.55 40.45 3.00e+00 1.11e-01 1.82e+02 angle pdb=" C SER A 729 " pdb=" CA SER A 729 " pdb=" HA SER A 729 " ideal model delta sigma weight residual 109.00 68.57 40.43 3.00e+00 1.11e-01 1.82e+02 ... (remaining 48747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.05: 11352 14.05 - 28.11: 1008 28.11 - 42.16: 262 42.16 - 56.21: 91 56.21 - 70.27: 29 Dihedral angle restraints: 12742 sinusoidal: 6956 harmonic: 5786 Sorted by residual: dihedral pdb=" CA PHE B 515 " pdb=" C PHE B 515 " pdb=" N MET B 516 " pdb=" CA MET B 516 " ideal model delta harmonic sigma weight residual 180.00 131.34 48.66 0 5.00e+00 4.00e-02 9.47e+01 dihedral pdb=" CA PHE A 515 " pdb=" C PHE A 515 " pdb=" N MET A 516 " pdb=" CA MET A 516 " ideal model delta harmonic sigma weight residual 180.00 131.36 48.64 0 5.00e+00 4.00e-02 9.46e+01 dihedral pdb=" CA LYS A 496 " pdb=" C LYS A 496 " pdb=" N ILE A 497 " pdb=" CA ILE A 497 " ideal model delta harmonic sigma weight residual -180.00 -140.88 -39.12 0 5.00e+00 4.00e-02 6.12e+01 ... (remaining 12739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 2038 0.156 - 0.312: 30 0.312 - 0.468: 6 0.468 - 0.624: 2 0.624 - 0.780: 6 Chirality restraints: 2082 Sorted by residual: chirality pdb=" CG LEU B 855 " pdb=" CB LEU B 855 " pdb=" CD1 LEU B 855 " pdb=" CD2 LEU B 855 " both_signs ideal model delta sigma weight residual False -2.59 -1.81 -0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" CG LEU A 855 " pdb=" CB LEU A 855 " pdb=" CD1 LEU A 855 " pdb=" CD2 LEU A 855 " both_signs ideal model delta sigma weight residual False -2.59 -1.81 -0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" CG LEU B 891 " pdb=" CB LEU B 891 " pdb=" CD1 LEU B 891 " pdb=" CD2 LEU B 891 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.29e+01 ... (remaining 2079 not shown) Planarity restraints: 4032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 610 " 0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO A 611 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 611 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 611 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 610 " -0.043 5.00e-02 4.00e+02 6.50e-02 6.77e+00 pdb=" N PRO B 611 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 611 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 611 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 626 " -0.040 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO A 627 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 627 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 627 " -0.033 5.00e-02 4.00e+02 ... (remaining 4029 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1502 2.19 - 2.79: 55890 2.79 - 3.39: 71650 3.39 - 4.00: 89507 4.00 - 4.60: 140392 Nonbonded interactions: 358941 Sorted by model distance: nonbonded pdb=" H2 MET B 1 " pdb=" HA MET B 1 " model vdw 1.582 1.816 nonbonded pdb=" H ALA A 862 " pdb=" HA ALA A 862 " model vdw 1.582 1.816 nonbonded pdb=" H SER A 729 " pdb=" HA SER A 729 " model vdw 1.588 1.816 nonbonded pdb=" H LEU A 15 " pdb=" HA LEU A 15 " model vdw 1.594 1.816 nonbonded pdb=" H LEU A 869 " pdb=" HA LEU A 869 " model vdw 1.595 1.816 ... (remaining 358936 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 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: 0.150 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.180 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 0.076 13718 Z= 0.442 Angle : 1.043 11.207 18604 Z= 0.600 Chirality : 0.073 0.780 2082 Planarity : 0.006 0.065 2424 Dihedral : 10.838 70.267 5092 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.27 % Allowed : 2.13 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -3.55 (0.18), residues: 1682 helix: -2.74 (0.13), residues: 846 sheet: -0.44 (0.93), residues: 24 loop : -1.87 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG B 527 TYR 0.035 0.004 TYR B 806 PHE 0.029 0.004 PHE B 479 TRP 0.021 0.003 TRP A 600 HIS 0.014 0.003 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00930 / 0.44 (13718) covalent geometry : angle 1.04287 / 0.60 (18604) hydrogen bonds : bond 0.29063 / 19.46 ( 602) hydrogen bonds : angle 9.84112 / 6.91 ( 1728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.353 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 ILE cc_start: 0.9313 (mt) cc_final: 0.9110 (tt) REVERT: A 500 ASP cc_start: 0.8088 (t0) cc_final: 0.7874 (t70) REVERT: A 718 MET cc_start: 0.7107 (mpt) cc_final: 0.6844 (mpp) REVERT: A 788 MET cc_start: 0.8500 (ptm) cc_final: 0.8210 (mmt) outliers start: 2 outliers final: 0 residues processed: 114 average time/residue: 0.2118 time to fit residues: 30.6685 Evaluate side-chains 69 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.2980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN A 128 ASN A 141 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 349 ASN ** A 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.087775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.068233 restraints weight = 107072.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.070923 restraints weight = 60078.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.072710 restraints weight = 40032.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.073886 restraints weight = 29923.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.074658 restraints weight = 24332.737| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13718 Z= 0.167 Angle : 0.802 11.200 18604 Z= 0.432 Chirality : 0.115 1.615 2082 Planarity : 0.006 0.064 2424 Dihedral : 7.484 34.422 1820 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.13 % Allowed : 1.06 % Favored : 98.80 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -2.94 (0.19), residues: 1682 helix: -1.94 (0.14), residues: 918 sheet: -0.37 (0.89), residues: 24 loop : -1.87 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 493 TYR 0.023 0.002 TYR A 740 PHE 0.018 0.002 PHE B 666 TRP 0.017 0.002 TRP B 600 HIS 0.010 0.002 HIS B 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (13718) covalent geometry : angle 0.80194 / 0.43 (18604) hydrogen bonds : bond 0.06417 / 4.28 ( 602) hydrogen bonds : angle 6.76416 / 4.77 ( 1728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.355 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: 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: symmetry clash revert: symmetry clash REVERT: B 35 MET cc_start: 0.9050 (ptp) cc_final: 0.8734 (ptp) REVERT: B 243 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8493 (mt-10) REVERT: B 323 ILE cc_start: 0.9444 (mt) cc_final: 0.9129 (tt) REVERT: B 500 ASP cc_start: 0.8136 (t0) cc_final: 0.7849 (t70) REVERT: B 762 GLN cc_start: 0.8559 (mt0) cc_final: 0.8247 (tm-30) REVERT: B 766 MET cc_start: 0.8498 (ttm) cc_final: 0.8273 (ttm) outliers start: 1 outliers final: 1 residues processed: 97 average time/residue: 0.1678 time to fit residues: 22.3505 Evaluate side-chains 74 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 150 optimal weight: 5.9990 chunk 15 optimal weight: 0.0170 chunk 95 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 chunk 74 optimal weight: 0.0060 chunk 56 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 overall best weight: 0.4234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 7 GLN B 108 ASN B 128 ASN B 141 ASN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN B 349 ASN B 637 HIS B 799 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.089044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.069130 restraints weight = 106616.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.072010 restraints weight = 58624.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.073945 restraints weight = 37937.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.075233 restraints weight = 27778.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.076065 restraints weight = 22409.305| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13718 Z= 0.128 Angle : 0.713 11.645 18604 Z= 0.382 Chirality : 0.120 1.675 2082 Planarity : 0.005 0.063 2424 Dihedral : 6.536 28.053 1820 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.38 % 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: -2.51 (0.19), residues: 1682 helix: -1.26 (0.15), residues: 954 sheet: -0.41 (0.85), residues: 24 loop : -2.17 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 493 TYR 0.020 0.002 TYR A 806 PHE 0.021 0.002 PHE A 666 TRP 0.011 0.001 TRP A 600 HIS 0.007 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (13718) covalent geometry : angle 0.71273 / 0.38 (18604) hydrogen bonds : bond 0.05106 / 3.39 ( 602) hydrogen bonds : angle 5.86166 / 4.15 ( 1728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.265 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 243 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8567 (mt-10) REVERT: B 323 ILE cc_start: 0.9474 (mt) cc_final: 0.9174 (tt) REVERT: B 461 MET cc_start: 0.8205 (mmp) cc_final: 0.7923 (mmm) REVERT: B 500 ASP cc_start: 0.8213 (t0) cc_final: 0.7941 (t70) REVERT: B 762 GLN cc_start: 0.8645 (mt0) cc_final: 0.8335 (tm-30) REVERT: B 766 MET cc_start: 0.8481 (ttm) cc_final: 0.8266 (ttm) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1529 time to fit residues: 19.3470 Evaluate side-chains 77 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 0.0000 chunk 98 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 146 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 355 GLN B 697 ASN B 734 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.087516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.067501 restraints weight = 107097.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.070291 restraints weight = 59713.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.071995 restraints weight = 38997.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.073249 restraints weight = 29171.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.073944 restraints weight = 23674.797| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13718 Z= 0.195 Angle : 0.752 13.366 18604 Z= 0.401 Chirality : 0.119 1.683 2082 Planarity : 0.012 0.383 2424 Dihedral : 6.637 47.244 1820 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.13 % Allowed : 0.66 % Favored : 99.20 % Cbeta Deviations : 0.38 % 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: -2.28 (0.19), residues: 1682 helix: -1.03 (0.16), residues: 954 sheet: -0.57 (0.79), residues: 24 loop : -2.15 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 13 TYR 0.015 0.001 TYR A 806 PHE 0.017 0.002 PHE A 666 TRP 0.010 0.001 TRP A 600 HIS 0.007 0.001 HIS A 654 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.20 (13718) covalent geometry : angle 0.75204 / 0.40 (18604) hydrogen bonds : bond 0.04702 / 3.12 ( 602) hydrogen bonds : angle 5.76046 / 4.08 ( 1728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.285 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: 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: symmetry clash revert: symmetry clash REVERT: B 243 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8542 (mt-10) REVERT: B 323 ILE cc_start: 0.9519 (mt) cc_final: 0.9227 (tt) REVERT: B 461 MET cc_start: 0.8354 (mmp) cc_final: 0.8052 (mmm) REVERT: B 500 ASP cc_start: 0.8349 (t0) cc_final: 0.8111 (t70) REVERT: B 762 GLN cc_start: 0.8610 (mt0) cc_final: 0.8337 (tm-30) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.1279 time to fit residues: 15.8544 Evaluate side-chains 75 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 159 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 chunk 125 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.088131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.068468 restraints weight = 105323.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.071268 restraints weight = 57020.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.073091 restraints weight = 36985.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.074304 restraints weight = 27282.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.075085 restraints weight = 22068.819| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13718 Z= 0.136 Angle : 0.690 11.741 18604 Z= 0.370 Chirality : 0.120 1.678 2082 Planarity : 0.005 0.066 2424 Dihedral : 6.138 25.029 1820 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.38 % 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: -2.00 (0.19), residues: 1682 helix: -0.68 (0.16), residues: 954 sheet: -0.63 (0.76), residues: 24 loop : -2.23 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 19 TYR 0.015 0.001 TYR A 806 PHE 0.017 0.002 PHE B 666 TRP 0.009 0.001 TRP A 600 HIS 0.008 0.001 HIS A 900 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (13718) covalent geometry : angle 0.68960 / 0.37 (18604) hydrogen bonds : bond 0.04246 / 2.80 ( 602) hydrogen bonds : angle 5.43172 / 3.85 ( 1728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.359 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: 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: 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 201 LEU cc_start: 0.8839 (tp) cc_final: 0.8634 (tp) REVERT: B 243 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8545 (mt-10) REVERT: B 323 ILE cc_start: 0.9490 (mt) cc_final: 0.9231 (tt) REVERT: B 461 MET cc_start: 0.8370 (mmp) cc_final: 0.8015 (mmm) REVERT: B 500 ASP cc_start: 0.8339 (t0) cc_final: 0.8062 (t70) REVERT: B 762 GLN cc_start: 0.8613 (mt0) cc_final: 0.8329 (tm-30) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1280 time to fit residues: 16.7676 Evaluate side-chains 76 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 65 optimal weight: 0.0070 chunk 164 optimal weight: 0.0470 chunk 67 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.088904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.069043 restraints weight = 105621.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.071927 restraints weight = 57445.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.073772 restraints weight = 37176.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.074968 restraints weight = 27469.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.075663 restraints weight = 22248.971| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13718 Z= 0.111 Angle : 0.668 11.759 18604 Z= 0.357 Chirality : 0.120 1.686 2082 Planarity : 0.005 0.064 2424 Dihedral : 5.780 23.636 1820 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.20), residues: 1682 helix: -0.41 (0.16), residues: 960 sheet: -0.74 (0.71), residues: 24 loop : -2.15 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 13 TYR 0.015 0.001 TYR B 806 PHE 0.020 0.002 PHE B 666 TRP 0.024 0.001 TRP A 600 HIS 0.006 0.001 HIS B 900 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (13718) covalent geometry : angle 0.66834 / 0.36 (18604) hydrogen bonds : bond 0.03906 / 2.55 ( 602) hydrogen bonds : angle 5.12977 / 3.64 ( 1728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.378 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 LEU cc_start: 0.8794 (tp) cc_final: 0.8556 (tp) REVERT: B 243 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8533 (mt-10) REVERT: B 323 ILE cc_start: 0.9464 (mt) cc_final: 0.9227 (tt) REVERT: B 461 MET cc_start: 0.8294 (mmp) cc_final: 0.7980 (mmm) REVERT: B 500 ASP cc_start: 0.8322 (t0) cc_final: 0.8027 (t70) REVERT: B 661 TYR cc_start: 0.4086 (p90) cc_final: 0.3333 (p90) REVERT: B 762 GLN cc_start: 0.8628 (mt0) cc_final: 0.8342 (tm-30) REVERT: B 766 MET cc_start: 0.8521 (ttm) cc_final: 0.8294 (ttm) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1408 time to fit residues: 18.4684 Evaluate side-chains 80 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 104 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 0.0370 chunk 109 optimal weight: 0.3980 overall best weight: 1.2864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.087817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.068289 restraints weight = 105670.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.071077 restraints weight = 57835.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.072881 restraints weight = 37288.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.074036 restraints weight = 27480.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.074731 restraints weight = 22225.767| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13718 Z= 0.142 Angle : 0.673 11.689 18604 Z= 0.361 Chirality : 0.118 1.680 2082 Planarity : 0.005 0.065 2424 Dihedral : 5.618 23.531 1820 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.20), residues: 1682 helix: -0.21 (0.17), residues: 960 sheet: -0.85 (0.69), residues: 24 loop : -2.21 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 13 TYR 0.017 0.001 TYR A 740 PHE 0.022 0.002 PHE A 666 TRP 0.014 0.001 TRP B 600 HIS 0.005 0.001 HIS B 900 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (13718) covalent geometry : angle 0.67344 / 0.36 (18604) hydrogen bonds : bond 0.03868 / 2.54 ( 602) hydrogen bonds : angle 5.17346 / 3.67 ( 1728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.237 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 ARG cc_start: 0.8012 (tpm170) cc_final: 0.7618 (ttm110) REVERT: B 201 LEU cc_start: 0.8839 (tp) cc_final: 0.8617 (tp) REVERT: B 243 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8496 (mt-10) REVERT: B 323 ILE cc_start: 0.9506 (mt) cc_final: 0.9265 (tt) REVERT: B 461 MET cc_start: 0.8266 (mmp) cc_final: 0.8029 (mmm) REVERT: B 500 ASP cc_start: 0.8310 (t0) cc_final: 0.8029 (t70) REVERT: B 762 GLN cc_start: 0.8598 (mt0) cc_final: 0.8317 (tm-30) REVERT: B 766 MET cc_start: 0.8537 (ttm) cc_final: 0.8312 (ttm) REVERT: B 813 ILE cc_start: 0.5948 (mt) cc_final: 0.5742 (mt) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1565 time to fit residues: 19.1838 Evaluate side-chains 80 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 105 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 103 optimal weight: 0.0060 chunk 164 optimal weight: 1.9990 chunk 127 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 20 optimal weight: 0.0870 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.089071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.069502 restraints weight = 106463.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.072263 restraints weight = 57839.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.074036 restraints weight = 37636.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.075259 restraints weight = 28030.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.076069 restraints weight = 22633.662| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13718 Z= 0.100 Angle : 0.647 11.781 18604 Z= 0.343 Chirality : 0.120 1.697 2082 Planarity : 0.005 0.064 2424 Dihedral : 5.345 22.730 1820 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.20), residues: 1682 helix: 0.13 (0.17), residues: 940 sheet: -0.77 (0.70), residues: 24 loop : -1.97 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 13 TYR 0.015 0.001 TYR A 288 PHE 0.022 0.001 PHE A 666 TRP 0.010 0.001 TRP A 530 HIS 0.005 0.001 HIS B 900 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (13718) covalent geometry : angle 0.64747 / 0.34 (18604) hydrogen bonds : bond 0.03625 / 2.38 ( 602) hydrogen bonds : angle 4.91891 / 3.49 ( 1728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.369 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 ARG cc_start: 0.8024 (tpm170) cc_final: 0.7680 (ttm110) REVERT: B 201 LEU cc_start: 0.8806 (tp) cc_final: 0.8595 (tp) REVERT: B 243 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8528 (mt-10) REVERT: B 323 ILE cc_start: 0.9494 (mt) cc_final: 0.9242 (tt) REVERT: B 461 MET cc_start: 0.8185 (mmp) cc_final: 0.7907 (mmm) REVERT: B 762 GLN cc_start: 0.8597 (mt0) cc_final: 0.8341 (tm-30) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1618 time to fit residues: 20.3074 Evaluate side-chains 81 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 48 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.0980 chunk 119 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 73 optimal weight: 0.0770 chunk 27 optimal weight: 0.5980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.089265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.069431 restraints weight = 106654.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.072280 restraints weight = 58118.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.074165 restraints weight = 37545.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.075418 restraints weight = 27592.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.076187 restraints weight = 22354.208| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13718 Z= 0.100 Angle : 0.638 11.632 18604 Z= 0.338 Chirality : 0.120 1.682 2082 Planarity : 0.005 0.064 2424 Dihedral : 5.127 22.229 1820 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.20), residues: 1682 helix: 0.31 (0.17), residues: 940 sheet: -0.91 (0.73), residues: 24 loop : -1.92 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 13 TYR 0.011 0.001 TYR A 806 PHE 0.020 0.001 PHE A 666 TRP 0.010 0.001 TRP A 530 HIS 0.004 0.001 HIS B 900 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (13718) covalent geometry : angle 0.63785 / 0.34 (18604) hydrogen bonds : bond 0.03460 / 2.27 ( 602) hydrogen bonds : angle 4.82635 / 3.43 ( 1728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.331 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 ARG cc_start: 0.8094 (tpm170) cc_final: 0.7741 (ttm110) REVERT: B 201 LEU cc_start: 0.8790 (tp) cc_final: 0.8565 (tp) REVERT: B 323 ILE cc_start: 0.9485 (mt) cc_final: 0.9249 (tt) REVERT: B 461 MET cc_start: 0.8237 (mmp) cc_final: 0.7964 (mmm) REVERT: B 762 GLN cc_start: 0.8559 (mt0) cc_final: 0.8293 (tm-30) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1697 time to fit residues: 21.4348 Evaluate side-chains 79 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 3 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 43 optimal weight: 0.0770 chunk 139 optimal weight: 0.5980 chunk 84 optimal weight: 10.0000 chunk 97 optimal weight: 0.5980 chunk 154 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.089111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.069501 restraints weight = 104891.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.072289 restraints weight = 56994.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.074080 restraints weight = 37187.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.075331 restraints weight = 27626.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.076132 restraints weight = 22326.814| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13718 Z= 0.102 Angle : 0.643 11.721 18604 Z= 0.342 Chirality : 0.121 1.716 2082 Planarity : 0.005 0.064 2424 Dihedral : 5.080 22.104 1820 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.20), residues: 1682 helix: 0.40 (0.17), residues: 942 sheet: -0.87 (0.75), residues: 24 loop : -1.87 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 559 TYR 0.012 0.001 TYR A 806 PHE 0.021 0.001 PHE A 666 TRP 0.009 0.001 TRP A 530 HIS 0.005 0.001 HIS A 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (13718) covalent geometry : angle 0.64349 / 0.34 (18604) hydrogen bonds : bond 0.03393 / 2.23 ( 602) hydrogen bonds : angle 4.80503 / 3.41 ( 1728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 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: 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: 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: symmetry clash REVERT: B 143 ARG cc_start: 0.8125 (tpm170) cc_final: 0.7752 (ttm110) REVERT: B 201 LEU cc_start: 0.8772 (tp) cc_final: 0.8561 (tp) REVERT: B 323 ILE cc_start: 0.9480 (mt) cc_final: 0.9258 (tt) REVERT: B 461 MET cc_start: 0.8180 (mmp) cc_final: 0.7928 (mmm) REVERT: B 762 GLN cc_start: 0.8549 (mt0) cc_final: 0.8292 (tm-30) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1568 time to fit residues: 19.9719 Evaluate side-chains 80 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 80 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 101 optimal weight: 0.0870 chunk 127 optimal weight: 0.0040 chunk 23 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 135 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.5572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.089161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.069569 restraints weight = 105204.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.072398 restraints weight = 57301.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.074240 restraints weight = 37098.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.075492 restraints weight = 27429.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.076264 restraints weight = 22096.385| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13718 Z= 0.102 Angle : 0.644 11.608 18604 Z= 0.341 Chirality : 0.120 1.683 2082 Planarity : 0.005 0.063 2424 Dihedral : 4.973 21.802 1820 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.20), residues: 1682 helix: 0.49 (0.17), residues: 942 sheet: -0.86 (0.78), residues: 24 loop : -1.87 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 559 TYR 0.014 0.001 TYR A 613 PHE 0.020 0.001 PHE A 666 TRP 0.009 0.001 TRP B 530 HIS 0.005 0.001 HIS A 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (13718) covalent geometry : angle 0.64444 / 0.34 (18604) hydrogen bonds : bond 0.03332 / 2.20 ( 602) hydrogen bonds : angle 4.75058 / 3.37 ( 1728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2654.43 seconds wall clock time: 46 minutes 43.76 seconds (2803.76 seconds total)