Starting phenix.real_space_refine on Sun May 25 08:27:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hae_34586/05_2025/8hae_34586.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hae_34586/05_2025/8hae_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hae_34586/05_2025/8hae_34586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hae_34586/05_2025/8hae_34586.map" model { file = "/net/cci-nas-00/data/ceres_data/8hae_34586/05_2025/8hae_34586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hae_34586/05_2025/8hae_34586.cif" } resolution = 4.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.44, per 1000 atoms: 0.47 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: 6.85 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.41 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: 9.41 Time building geometry restraints manager: 8.23 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: 0.08 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: 1.700 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: 0.420 Extract box with map and model: 0.900 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 54.220 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 6.14 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.021 0.003 TRP A 600 HIS 0.014 0.003 HIS A 279 PHE 0.029 0.004 PHE B 479 TYR 0.035 0.004 TYR B 806 ARG 0.020 0.002 ARG B 527 Details of bonding type rmsd hydrogen bonds : bond 0.29063 ( 602) hydrogen bonds : angle 9.84112 ( 1728) covalent geometry : bond 0.00930 (13718) covalent geometry : angle 1.04287 (18604) *********************** 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 : 1.107 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: 0.4965 time to fit residues: 72.1788 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 : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.9990 chunk 127 optimal weight: 0.0040 chunk 70 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 68 optimal weight: 0.0170 chunk 131 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 overall best weight: 0.4430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 128 ASN B 141 ASN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN B 637 HIS ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 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 = 0.3915 r_free = 0.3915 target = 0.088712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.068693 restraints weight = 103383.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.071534 restraints weight = 56788.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.073376 restraints weight = 37249.405| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13718 Z= 0.154 Angle : 0.792 11.461 18604 Z= 0.425 Chirality : 0.116 1.629 2082 Planarity : 0.006 0.063 2424 Dihedral : 7.361 33.188 1820 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.13 % Allowed : 0.80 % Favored : 99.07 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.19), residues: 1682 helix: -1.89 (0.14), residues: 942 sheet: -0.35 (0.89), residues: 24 loop : -1.96 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 364 HIS 0.009 0.001 HIS A 279 PHE 0.018 0.002 PHE B 666 TYR 0.024 0.002 TYR B 740 ARG 0.007 0.001 ARG B 493 Details of bonding type rmsd hydrogen bonds : bond 0.06198 ( 602) hydrogen bonds : angle 6.60261 ( 1728) covalent geometry : bond 0.00321 (13718) covalent geometry : angle 0.79205 (18604) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 1.039 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 243 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8586 (mt-10) REVERT: B 453 SER cc_start: 0.9401 (m) cc_final: 0.9056 (p) REVERT: B 471 MET cc_start: 0.7877 (ttt) cc_final: 0.7187 (tpp) REVERT: B 500 ASP cc_start: 0.8101 (t0) cc_final: 0.7836 (t70) REVERT: B 762 GLN cc_start: 0.8594 (mt0) cc_final: 0.8018 (tm-30) REVERT: B 766 MET cc_start: 0.8478 (ttm) cc_final: 0.8274 (ttm) outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.4059 time to fit residues: 54.3980 Evaluate side-chains 80 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 133 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 161 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 112 optimal weight: 0.1980 chunk 53 optimal weight: 10.0000 chunk 2 optimal weight: 0.0670 chunk 87 optimal weight: 0.7980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.088427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.068762 restraints weight = 103966.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.071599 restraints weight = 56812.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.073446 restraints weight = 36849.291| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13718 Z= 0.137 Angle : 0.732 11.505 18604 Z= 0.389 Chirality : 0.116 1.660 2082 Planarity : 0.010 0.315 2424 Dihedral : 6.953 39.411 1820 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.25 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.18), residues: 1682 helix: -1.81 (0.14), residues: 932 sheet: -0.80 (0.82), residues: 24 loop : -2.20 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 600 HIS 0.007 0.001 HIS A 279 PHE 0.019 0.001 PHE B 666 TYR 0.018 0.001 TYR A 806 ARG 0.008 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.05237 ( 602) hydrogen bonds : angle 6.08610 ( 1728) covalent geometry : bond 0.00289 (13718) covalent geometry : angle 0.73167 (18604) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 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 : 1.116 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 461 MET cc_start: 0.8093 (mmp) cc_final: 0.7871 (mmm) REVERT: B 500 ASP cc_start: 0.8165 (t0) cc_final: 0.7945 (t70) REVERT: B 762 GLN cc_start: 0.8599 (mt0) cc_final: 0.8308 (tm-30) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.3644 time to fit residues: 45.6406 Evaluate side-chains 73 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 76 optimal weight: 4.9990 chunk 147 optimal weight: 0.0770 chunk 5 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 150 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 GLN ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.087712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.068087 restraints weight = 106511.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.070846 restraints weight = 58145.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.072563 restraints weight = 37987.981| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13718 Z= 0.166 Angle : 0.714 11.169 18604 Z= 0.385 Chirality : 0.118 1.679 2082 Planarity : 0.005 0.065 2424 Dihedral : 6.434 26.112 1820 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.18), residues: 1682 helix: -1.76 (0.14), residues: 940 sheet: -1.08 (0.71), residues: 24 loop : -2.43 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 600 HIS 0.007 0.001 HIS B 654 PHE 0.019 0.002 PHE B 666 TYR 0.017 0.001 TYR B 806 ARG 0.005 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.04560 ( 602) hydrogen bonds : angle 5.78226 ( 1728) covalent geometry : bond 0.00353 (13718) covalent geometry : angle 0.71420 (18604) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 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 : 1.014 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: 0.8880 (mt-10) cc_final: 0.8555 (mt-10) REVERT: B 461 MET cc_start: 0.8375 (mmp) cc_final: 0.8058 (mmm) REVERT: B 500 ASP cc_start: 0.8286 (t0) cc_final: 0.8009 (t70) REVERT: B 762 GLN cc_start: 0.8599 (mt0) cc_final: 0.8335 (tm-30) REVERT: B 766 MET cc_start: 0.8500 (ttm) cc_final: 0.8298 (ttm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.3503 time to fit residues: 44.3041 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 : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 15 optimal weight: 0.0270 chunk 109 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 2 optimal weight: 0.0270 chunk 108 optimal weight: 0.3980 chunk 148 optimal weight: 9.9990 chunk 48 optimal weight: 0.0030 chunk 36 optimal weight: 0.9990 chunk 83 optimal weight: 0.2980 overall best weight: 0.1506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.089572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.069727 restraints weight = 105466.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.072677 restraints weight = 56811.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.074569 restraints weight = 36670.740| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4430 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= 0.108 Angle : 0.657 11.427 18604 Z= 0.349 Chirality : 0.118 1.691 2082 Planarity : 0.004 0.063 2424 Dihedral : 5.840 24.769 1820 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.18), residues: 1682 helix: -1.27 (0.15), residues: 954 sheet: -1.19 (0.65), residues: 24 loop : -2.56 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 530 HIS 0.004 0.001 HIS A 70 PHE 0.022 0.001 PHE A 666 TYR 0.019 0.001 TYR A 740 ARG 0.004 0.000 ARG B 13 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 602) hydrogen bonds : angle 5.15724 ( 1728) covalent geometry : bond 0.00237 (13718) covalent geometry : angle 0.65714 (18604) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.993 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 243 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8557 (mt-10) REVERT: B 461 MET cc_start: 0.8349 (mmp) cc_final: 0.8034 (mmm) REVERT: B 500 ASP cc_start: 0.8208 (t0) cc_final: 0.7940 (t70) REVERT: B 762 GLN cc_start: 0.8620 (mt0) cc_final: 0.8354 (tm-30) REVERT: B 766 MET cc_start: 0.8528 (ttm) cc_final: 0.8305 (ttm) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.3539 time to fit residues: 45.7916 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 : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 119 optimal weight: 0.0980 chunk 132 optimal weight: 0.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 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 = 0.3922 r_free = 0.3922 target = 0.088753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.068960 restraints weight = 109226.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.071742 restraints weight = 59115.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.073463 restraints weight = 38641.794| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13718 Z= 0.147 Angle : 0.679 11.122 18604 Z= 0.364 Chirality : 0.116 1.688 2082 Planarity : 0.005 0.063 2424 Dihedral : 5.675 23.741 1820 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.18), residues: 1682 helix: -1.22 (0.15), residues: 944 sheet: -1.45 (0.66), residues: 24 loop : -2.40 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 600 HIS 0.008 0.001 HIS B 900 PHE 0.022 0.002 PHE A 666 TYR 0.014 0.001 TYR A 806 ARG 0.003 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 602) hydrogen bonds : angle 5.20702 ( 1728) covalent geometry : bond 0.00312 (13718) covalent geometry : angle 0.67890 (18604) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 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 : 0.968 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: A 243 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8567 (mp0) REVERT: A 323 ILE cc_start: 0.9477 (mt) cc_final: 0.9276 (tt) REVERT: A 461 MET cc_start: 0.8486 (mmp) cc_final: 0.8165 (mmm) REVERT: A 500 ASP cc_start: 0.8276 (t0) cc_final: 0.7971 (t70) REVERT: A 762 GLN cc_start: 0.8676 (mt0) cc_final: 0.8227 (tm-30) REVERT: A 813 ILE cc_start: 0.6287 (mt) cc_final: 0.5984 (mt) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.3542 time to fit residues: 43.5061 Evaluate side-chains 78 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 99 optimal weight: 0.4980 chunk 78 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 119 optimal weight: 0.0970 chunk 131 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 53 optimal weight: 0.0370 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.089390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.069684 restraints weight = 105484.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.072538 restraints weight = 56643.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.074356 restraints weight = 36609.028| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4858 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= 0.101 Angle : 0.647 11.712 18604 Z= 0.344 Chirality : 0.120 1.753 2082 Planarity : 0.004 0.064 2424 Dihedral : 5.459 23.199 1820 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.18), residues: 1682 helix: -1.03 (0.15), residues: 952 sheet: -1.35 (0.69), residues: 24 loop : -2.41 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 600 HIS 0.006 0.001 HIS A 900 PHE 0.019 0.001 PHE A 666 TYR 0.014 0.001 TYR A 740 ARG 0.003 0.000 ARG B 13 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 602) hydrogen bonds : angle 4.99302 ( 1728) covalent geometry : bond 0.00221 (13718) covalent geometry : angle 0.64665 (18604) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 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: 0 poor density : 86 time to evaluate : 1.013 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: B 201 LEU cc_start: 0.8808 (tp) cc_final: 0.8601 (tp) REVERT: B 243 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8546 (mt-10) REVERT: B 461 MET cc_start: 0.8349 (mmp) cc_final: 0.8005 (mmm) REVERT: B 500 ASP cc_start: 0.8193 (t0) cc_final: 0.7929 (t70) REVERT: B 762 GLN cc_start: 0.8582 (mt0) cc_final: 0.8331 (tm-30) REVERT: B 766 MET cc_start: 0.8593 (ttm) cc_final: 0.8364 (ttm) REVERT: B 813 ILE cc_start: 0.6144 (mt) cc_final: 0.5800 (mt) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.3319 time to fit residues: 40.0894 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 : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 74 optimal weight: 0.3980 chunk 136 optimal weight: 0.0170 chunk 133 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 41 optimal weight: 0.0050 overall best weight: 0.3232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3936 r_free = 0.3936 target = 0.089574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.070097 restraints weight = 104972.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.072970 restraints weight = 56591.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.074810 restraints weight = 36429.651| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5171 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= 0.098 Angle : 0.639 11.746 18604 Z= 0.338 Chirality : 0.120 1.692 2082 Planarity : 0.004 0.063 2424 Dihedral : 5.162 22.177 1820 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.19), residues: 1682 helix: -0.65 (0.16), residues: 930 sheet: -1.31 (0.75), residues: 24 loop : -2.35 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 530 HIS 0.005 0.001 HIS A 900 PHE 0.022 0.001 PHE A 666 TYR 0.013 0.001 TYR B 806 ARG 0.002 0.000 ARG B 13 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 602) hydrogen bonds : angle 4.79892 ( 1728) covalent geometry : bond 0.00219 (13718) covalent geometry : angle 0.63894 (18604) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 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 : 1.020 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: B 201 LEU cc_start: 0.8784 (tp) cc_final: 0.8570 (tp) REVERT: B 243 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8484 (mp0) REVERT: B 461 MET cc_start: 0.8407 (mmp) cc_final: 0.8005 (mmm) REVERT: B 500 ASP cc_start: 0.8173 (t0) cc_final: 0.7928 (t70) REVERT: B 762 GLN cc_start: 0.8618 (mt0) cc_final: 0.8377 (tm-30) REVERT: B 766 MET cc_start: 0.8619 (ttm) cc_final: 0.8378 (ttm) REVERT: B 813 ILE cc_start: 0.6029 (mt) cc_final: 0.5674 (mt) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.3670 time to fit residues: 44.3815 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 : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 166 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 167 optimal weight: 0.9980 chunk 117 optimal weight: 0.3980 chunk 120 optimal weight: 0.9980 chunk 121 optimal weight: 0.1980 chunk 164 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 3 optimal weight: 0.0370 chunk 13 optimal weight: 0.5980 chunk 15 optimal weight: 0.2980 overall best weight: 0.2658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3940 r_free = 0.3940 target = 0.089752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.070197 restraints weight = 104735.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.073041 restraints weight = 56180.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.074904 restraints weight = 36305.254| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.5408 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= 0.095 Angle : 0.634 11.758 18604 Z= 0.334 Chirality : 0.120 1.720 2082 Planarity : 0.004 0.063 2424 Dihedral : 4.973 21.542 1820 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.19), residues: 1682 helix: -0.38 (0.16), residues: 930 sheet: -1.16 (0.83), residues: 24 loop : -2.29 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 530 HIS 0.005 0.001 HIS A 558 PHE 0.022 0.001 PHE A 666 TYR 0.012 0.001 TYR A 806 ARG 0.007 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.03292 ( 602) hydrogen bonds : angle 4.71920 ( 1728) covalent geometry : bond 0.00213 (13718) covalent geometry : angle 0.63434 (18604) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 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 : 0.985 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: B 201 LEU cc_start: 0.8753 (tp) cc_final: 0.8534 (tp) REVERT: B 461 MET cc_start: 0.8355 (mmp) cc_final: 0.7941 (mmm) REVERT: B 500 ASP cc_start: 0.8149 (t0) cc_final: 0.7929 (t70) REVERT: B 762 GLN cc_start: 0.8581 (mt0) cc_final: 0.8332 (tm-30) REVERT: B 766 MET cc_start: 0.8565 (ttm) cc_final: 0.8330 (ttm) REVERT: B 813 ILE cc_start: 0.5919 (mt) cc_final: 0.5657 (mt) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.3192 time to fit residues: 40.1824 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 : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 64 optimal weight: 8.9990 chunk 157 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 150 optimal weight: 0.1980 chunk 152 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 46 optimal weight: 0.0770 chunk 128 optimal weight: 0.0870 chunk 114 optimal weight: 3.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** 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 = 0.3943 r_free = 0.3943 target = 0.089836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.070262 restraints weight = 107848.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.073069 restraints weight = 58357.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.074876 restraints weight = 38211.628| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5518 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 : 0.633 11.738 18604 Z= 0.334 Chirality : 0.120 1.705 2082 Planarity : 0.004 0.062 2424 Dihedral : 4.884 21.350 1820 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.19), residues: 1682 helix: -0.26 (0.16), residues: 918 sheet: -1.04 (0.86), residues: 24 loop : -2.23 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 530 HIS 0.005 0.001 HIS A 558 PHE 0.023 0.001 PHE B 666 TYR 0.012 0.001 TYR A 806 ARG 0.004 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 602) hydrogen bonds : angle 4.71267 ( 1728) covalent geometry : bond 0.00221 (13718) covalent geometry : angle 0.63337 (18604) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 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 : 1.051 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: A 201 LEU cc_start: 0.8808 (tp) cc_final: 0.8582 (tp) REVERT: A 243 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8515 (mp0) REVERT: A 461 MET cc_start: 0.8479 (mmp) cc_final: 0.8033 (mmm) REVERT: A 500 ASP cc_start: 0.8034 (t0) cc_final: 0.7785 (t70) REVERT: A 762 GLN cc_start: 0.8632 (mt0) cc_final: 0.8219 (tm-30) REVERT: A 766 MET cc_start: 0.8505 (ttm) cc_final: 0.8263 (ttm) REVERT: A 813 ILE cc_start: 0.6031 (mt) cc_final: 0.5752 (mt) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.3004 time to fit residues: 39.2327 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 : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 136 optimal weight: 9.9990 chunk 18 optimal weight: 0.0470 chunk 50 optimal weight: 10.0000 chunk 20 optimal weight: 0.0010 chunk 12 optimal weight: 5.9990 chunk 106 optimal weight: 0.0270 chunk 80 optimal weight: 0.4980 chunk 90 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.2542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3955 r_free = 0.3955 target = 0.090522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.070771 restraints weight = 106658.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.073651 restraints weight = 58016.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.075512 restraints weight = 37876.010| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.5717 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= 0.095 Angle : 0.632 12.227 18604 Z= 0.333 Chirality : 0.121 1.714 2082 Planarity : 0.004 0.062 2424 Dihedral : 4.764 21.004 1820 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.19), residues: 1682 helix: -0.16 (0.17), residues: 932 sheet: -1.53 (0.90), residues: 24 loop : -2.26 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 530 HIS 0.005 0.001 HIS B 900 PHE 0.022 0.001 PHE B 666 TYR 0.012 0.001 TYR B 806 ARG 0.003 0.000 ARG B 559 Details of bonding type rmsd hydrogen bonds : bond 0.03140 ( 602) hydrogen bonds : angle 4.62783 ( 1728) covalent geometry : bond 0.00215 (13718) covalent geometry : angle 0.63201 (18604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4877.82 seconds wall clock time: 85 minutes 45.67 seconds (5145.67 seconds total)