Starting phenix.real_space_refine on Mon Aug 25 08:34:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hae_34586/08_2025/8hae_34586.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hae_34586/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hae_34586/08_2025/8hae_34586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hae_34586/08_2025/8hae_34586.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hae_34586/08_2025/8hae_34586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hae_34586/08_2025/8hae_34586.map" } resolution = 4.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 98 5.16 5 C 8498 2.51 5 N 2322 2.21 5 O 2508 1.98 5 H 13272 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26698 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 13349 Classifications: {'peptide': 845} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 39, 'TRANS': 805} Chain breaks: 1 Chain: "B" Number of atoms: 13349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 13349 Classifications: {'peptide': 845} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 39, 'TRANS': 805} Chain breaks: 1 Time building chain proxies: 4.74, per 1000 atoms: 0.18 Number of scatterers: 26698 At special positions: 0 Unit cell: (164.813, 133.052, 83.2648, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 O 2508 8.00 N 2322 7.00 C 8498 6.00 H 13272 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 799.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 10 sheets defined 64.9% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 1 through 4 removed outlier: 3.945A pdb=" N ALA A 4 " --> pdb=" O MET A 1 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1 through 4' Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 26 through 40 Proline residue: A 36 - end of helix Processing helix chain 'A' and resid 67 through 76 removed outlier: 3.844A pdb=" N ALA A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN A 74 " --> pdb=" O HIS A 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N CYS A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 110 through 118 removed outlier: 3.590A pdb=" N MET A 114 " --> pdb=" O GLN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 142 removed outlier: 3.693A pdb=" N ASN A 141 " --> pdb=" O TRP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 149 Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 166 through 175 removed outlier: 3.933A pdb=" N CYS A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 173 " --> pdb=" O HIS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.811A pdb=" N GLN A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 208 removed outlier: 3.505A pdb=" N PHE A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 206 " --> pdb=" O TYR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 removed outlier: 3.541A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 removed outlier: 3.622A pdb=" N CYS A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 252 removed outlier: 3.679A pdb=" N TYR A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 265 removed outlier: 3.654A pdb=" N ILE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 282 removed outlier: 4.396A pdb=" N LEU A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 308 Processing helix chain 'A' and resid 314 through 334 removed outlier: 3.534A pdb=" N ILE A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 381 Proline residue: A 359 - end of helix removed outlier: 4.222A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 462 removed outlier: 3.771A pdb=" N VAL A 455 " --> pdb=" O ARG A 451 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR A 460 " --> pdb=" O ILE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 492 removed outlier: 3.867A pdb=" N ILE A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU A 485 " --> pdb=" O CYS A 481 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 508 removed outlier: 3.752A pdb=" N GLU A 507 " --> pdb=" O HIS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 522 removed outlier: 4.373A pdb=" N ARG A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N HIS A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 519 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 526 removed outlier: 3.645A pdb=" N ASP A 526 " --> pdb=" O PRO A 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 523 through 526' Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 561 through 571 removed outlier: 3.764A pdb=" N CYS A 567 " --> pdb=" O PHE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 593 through 608 removed outlier: 3.742A pdb=" N ASN A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 635 removed outlier: 4.247A pdb=" N TYR A 632 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 634 " --> pdb=" O SER A 631 " (cutoff:3.500A) Proline residue: A 635 - end of helix Processing helix chain 'A' and resid 636 through 654 removed outlier: 3.643A pdb=" N ASN A 653 " --> pdb=" O GLY A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 672 removed outlier: 3.809A pdb=" N TYR A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 683 Processing helix chain 'A' and resid 684 through 697 removed outlier: 3.945A pdb=" N ASN A 690 " --> pdb=" O GLU A 686 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN A 697 " --> pdb=" O TRP A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 703 removed outlier: 4.425A pdb=" N GLY A 703 " --> pdb=" O ILE A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 730 removed outlier: 3.749A pdb=" N ILE A 730 " --> pdb=" O GLY A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 735 No H-bonds generated for 'chain 'A' and resid 733 through 735' Processing helix chain 'A' and resid 736 through 750 removed outlier: 4.322A pdb=" N VAL A 741 " --> pdb=" O LYS A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 765 removed outlier: 3.789A pdb=" N GLN A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 758 " --> pdb=" O GLN A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 776 removed outlier: 4.171A pdb=" N LEU A 775 " --> pdb=" O LEU A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 782 removed outlier: 4.153A pdb=" N GLU A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 792 through 799 Processing helix chain 'A' and resid 810 through 821 Processing helix chain 'A' and resid 824 through 837 removed outlier: 4.544A pdb=" N LEU A 830 " --> pdb=" O GLU A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 849 Processing helix chain 'A' and resid 887 through 901 removed outlier: 4.526A pdb=" N LEU A 896 " --> pdb=" O LYS A 892 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N CYS A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 4 removed outlier: 3.944A pdb=" N ALA B 4 " --> pdb=" O MET B 1 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1 through 4' Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 26 through 40 Proline residue: B 36 - end of helix Processing helix chain 'B' and resid 67 through 76 removed outlier: 3.844A pdb=" N ALA B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN B 74 " --> pdb=" O HIS B 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N CYS B 75 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 110 through 118 removed outlier: 3.589A pdb=" N MET B 114 " --> pdb=" O GLN B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 142 removed outlier: 3.693A pdb=" N ASN B 141 " --> pdb=" O TRP B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 149 Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 166 through 175 removed outlier: 3.933A pdb=" N CYS B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 173 " --> pdb=" O HIS B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.812A pdb=" N GLN B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 183 " --> pdb=" O THR B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 208 removed outlier: 3.506A pdb=" N PHE B 203 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 204 " --> pdb=" O PRO B 200 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B 206 " --> pdb=" O TYR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 220 removed outlier: 3.541A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 removed outlier: 3.623A pdb=" N CYS B 236 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 252 removed outlier: 3.680A pdb=" N TYR B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 265 removed outlier: 3.653A pdb=" N ILE B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN B 265 " --> pdb=" O GLN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 282 removed outlier: 4.396A pdb=" N LEU B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 308 Processing helix chain 'B' and resid 314 through 334 removed outlier: 3.534A pdb=" N ILE B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 381 Proline residue: B 359 - end of helix removed outlier: 4.222A pdb=" N LEU B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 376 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 462 removed outlier: 3.770A pdb=" N VAL B 455 " --> pdb=" O ARG B 451 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR B 460 " --> pdb=" O ILE B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 492 removed outlier: 3.867A pdb=" N ILE B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS B 482 " --> pdb=" O GLU B 478 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU B 485 " --> pdb=" O CYS B 481 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 508 removed outlier: 3.753A pdb=" N GLU B 507 " --> pdb=" O HIS B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 522 removed outlier: 4.371A pdb=" N ARG B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N HIS B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE B 518 " --> pdb=" O ARG B 514 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE B 519 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 526 removed outlier: 3.645A pdb=" N ASP B 526 " --> pdb=" O PRO B 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 523 through 526' Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 532 through 537 Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 558 through 560 No H-bonds generated for 'chain 'B' and resid 558 through 560' Processing helix chain 'B' and resid 561 through 571 removed outlier: 3.764A pdb=" N CYS B 567 " --> pdb=" O PHE B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 579 Processing helix chain 'B' and resid 593 through 608 removed outlier: 3.742A pdb=" N ASN B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 635 removed outlier: 4.247A pdb=" N TYR B 632 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN B 634 " --> pdb=" O SER B 631 " (cutoff:3.500A) Proline residue: B 635 - end of helix Processing helix chain 'B' and resid 636 through 654 removed outlier: 3.642A pdb=" N ASN B 653 " --> pdb=" O GLY B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 672 removed outlier: 3.809A pdb=" N TYR B 667 " --> pdb=" O THR B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 683 Processing helix chain 'B' and resid 684 through 697 removed outlier: 3.945A pdb=" N ASN B 690 " --> pdb=" O GLU B 686 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 697 " --> pdb=" O TRP B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 703 removed outlier: 4.425A pdb=" N GLY B 703 " --> pdb=" O ILE B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 730 removed outlier: 3.751A pdb=" N ILE B 730 " --> pdb=" O GLY B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 735 No H-bonds generated for 'chain 'B' and resid 733 through 735' Processing helix chain 'B' and resid 736 through 750 removed outlier: 4.321A pdb=" N VAL B 741 " --> pdb=" O LYS B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 765 removed outlier: 3.790A pdb=" N GLN B 756 " --> pdb=" O ALA B 752 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN B 758 " --> pdb=" O GLN B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 776 removed outlier: 4.171A pdb=" N LEU B 775 " --> pdb=" O LEU B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 782 removed outlier: 4.153A pdb=" N GLU B 782 " --> pdb=" O GLU B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 787 Processing helix chain 'B' and resid 792 through 799 Processing helix chain 'B' and resid 810 through 821 Processing helix chain 'B' and resid 824 through 837 removed outlier: 4.544A pdb=" N LEU B 830 " --> pdb=" O GLU B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 849 Processing helix chain 'B' and resid 887 through 901 removed outlier: 4.526A pdb=" N LEU B 896 " --> pdb=" O LYS B 892 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 897 " --> pdb=" O ASP B 893 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N CYS B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 336 through 337 removed outlier: 4.723A pdb=" N GLY A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 554 through 557 Processing sheet with id=AA3, first strand: chain 'A' and resid 616 through 617 Processing sheet with id=AA4, first strand: chain 'A' and resid 709 through 713 Processing sheet with id=AA5, first strand: chain 'A' and resid 801 through 803 removed outlier: 6.768A pdb=" N GLU A 801 " --> pdb=" O ILE A 860 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ALA A 862 " --> pdb=" O GLU A 801 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR A 803 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 336 through 337 removed outlier: 4.722A pdb=" N GLY B 341 " --> pdb=" O SER B 337 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 554 through 557 Processing sheet with id=AA8, first strand: chain 'B' and resid 616 through 617 Processing sheet with id=AA9, first strand: chain 'B' and resid 709 through 713 Processing sheet with id=AB1, first strand: chain 'B' and resid 801 through 803 removed outlier: 6.768A pdb=" N GLU B 801 " --> pdb=" O ILE B 860 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ALA B 862 " --> pdb=" O GLU B 801 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR B 803 " --> pdb=" O ALA B 862 " (cutoff:3.500A) 602 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.38 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 13228 1.03 - 1.22: 48 1.22 - 1.42: 5747 1.42 - 1.62: 7815 1.62 - 1.82: 152 Bond restraints: 26990 Sorted by residual: bond pdb=" CA VAL A 741 " pdb=" HA VAL A 741 " ideal model delta sigma weight residual 0.970 0.914 0.056 2.00e-02 2.50e+03 7.98e+00 bond pdb=" CD LYS A 798 " pdb=" CE LYS A 798 " ideal model delta sigma weight residual 1.520 1.596 -0.076 3.00e-02 1.11e+03 6.40e+00 bond pdb=" CD LYS B 798 " pdb=" CE LYS B 798 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.22e+00 bond pdb=" CG2 THR B 707 " pdb="HG22 THR B 707 " ideal model delta sigma weight residual 0.970 1.016 -0.046 2.00e-02 2.50e+03 5.22e+00 bond pdb=" CD ARG B 44 " pdb=" NE ARG B 44 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.40e-02 5.10e+03 4.66e+00 ... (remaining 26985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.68: 48666 8.68 - 17.35: 6 17.35 - 26.03: 3 26.03 - 34.71: 38 34.71 - 43.38: 39 Bond angle restraints: 48752 Sorted by residual: angle pdb=" N VAL A 741 " pdb=" CA VAL A 741 " pdb=" HA VAL A 741 " ideal model delta sigma weight residual 110.00 66.62 43.38 3.00e+00 1.11e-01 2.09e+02 angle pdb=" C GLU A 25 " pdb=" CA GLU A 25 " pdb=" HA GLU A 25 " ideal model delta sigma weight residual 109.00 66.02 42.98 3.00e+00 1.11e-01 2.05e+02 angle pdb=" C LEU A 869 " pdb=" CA LEU A 869 " pdb=" HA LEU A 869 " ideal model delta sigma weight residual 109.00 68.22 40.78 3.00e+00 1.11e-01 1.85e+02 angle pdb=" C PHE A 708 " pdb=" CA PHE A 708 " pdb=" HA PHE A 708 " ideal model delta sigma weight residual 109.00 68.55 40.45 3.00e+00 1.11e-01 1.82e+02 angle pdb=" C SER A 729 " pdb=" CA SER A 729 " pdb=" HA SER A 729 " ideal model delta sigma weight residual 109.00 68.57 40.43 3.00e+00 1.11e-01 1.82e+02 ... (remaining 48747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.05: 11352 14.05 - 28.11: 1008 28.11 - 42.16: 262 42.16 - 56.21: 91 56.21 - 70.27: 29 Dihedral angle restraints: 12742 sinusoidal: 6956 harmonic: 5786 Sorted by residual: dihedral pdb=" CA PHE B 515 " pdb=" C PHE B 515 " pdb=" N MET B 516 " pdb=" CA MET B 516 " ideal model delta harmonic sigma weight residual 180.00 131.34 48.66 0 5.00e+00 4.00e-02 9.47e+01 dihedral pdb=" CA PHE A 515 " pdb=" C PHE A 515 " pdb=" N MET A 516 " pdb=" CA MET A 516 " ideal model delta harmonic sigma weight residual 180.00 131.36 48.64 0 5.00e+00 4.00e-02 9.46e+01 dihedral pdb=" CA LYS A 496 " pdb=" C LYS A 496 " pdb=" N ILE A 497 " pdb=" CA ILE A 497 " ideal model delta harmonic sigma weight residual -180.00 -140.88 -39.12 0 5.00e+00 4.00e-02 6.12e+01 ... (remaining 12739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 2038 0.156 - 0.312: 30 0.312 - 0.468: 6 0.468 - 0.624: 2 0.624 - 0.780: 6 Chirality restraints: 2082 Sorted by residual: chirality pdb=" CG LEU B 855 " pdb=" CB LEU B 855 " pdb=" CD1 LEU B 855 " pdb=" CD2 LEU B 855 " both_signs ideal model delta sigma weight residual False -2.59 -1.81 -0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" CG LEU A 855 " pdb=" CB LEU A 855 " pdb=" CD1 LEU A 855 " pdb=" CD2 LEU A 855 " both_signs ideal model delta sigma weight residual False -2.59 -1.81 -0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" CG LEU B 891 " pdb=" CB LEU B 891 " pdb=" CD1 LEU B 891 " pdb=" CD2 LEU B 891 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.29e+01 ... (remaining 2079 not shown) Planarity restraints: 4032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 610 " 0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO A 611 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 611 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 611 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 610 " -0.043 5.00e-02 4.00e+02 6.50e-02 6.77e+00 pdb=" N PRO B 611 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 611 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 611 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 626 " -0.040 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO A 627 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 627 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 627 " -0.033 5.00e-02 4.00e+02 ... (remaining 4029 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1502 2.19 - 2.79: 55890 2.79 - 3.39: 71650 3.39 - 4.00: 89507 4.00 - 4.60: 140392 Nonbonded interactions: 358941 Sorted by model distance: nonbonded pdb=" H2 MET B 1 " pdb=" HA MET B 1 " model vdw 1.582 1.816 nonbonded pdb=" H ALA A 862 " pdb=" HA ALA A 862 " model vdw 1.582 1.816 nonbonded pdb=" H SER A 729 " pdb=" HA SER A 729 " model vdw 1.588 1.816 nonbonded pdb=" H LEU A 15 " pdb=" HA LEU A 15 " model vdw 1.594 1.816 nonbonded pdb=" H LEU A 869 " pdb=" HA LEU A 869 " model vdw 1.595 1.816 ... (remaining 358936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 0.480 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.510 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.440 ------------------------------------------------------------------------------- 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 : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.27 % Allowed : 2.13 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.55 (0.18), residues: 1682 helix: -2.74 (0.13), residues: 846 sheet: -0.44 (0.93), residues: 24 loop : -1.87 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG B 527 TYR 0.035 0.004 TYR B 806 PHE 0.029 0.004 PHE B 479 TRP 0.021 0.003 TRP A 600 HIS 0.014 0.003 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00930 (13718) covalent geometry : angle 1.04287 (18604) hydrogen bonds : bond 0.29063 ( 602) hydrogen bonds : angle 9.84112 ( 1728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.304 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: 0.2146 time to fit residues: 30.8417 Evaluate side-chains 69 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.2980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 302 ASN B 349 ASN ** B 637 HIS ** 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 = 0.3901 r_free = 0.3901 target = 0.087764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.068211 restraints weight = 107061.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.070954 restraints weight = 60629.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.072757 restraints weight = 39906.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.073937 restraints weight = 29662.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.074704 restraints weight = 24192.154| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13718 Z= 0.167 Angle : 0.802 11.200 18604 Z= 0.432 Chirality : 0.115 1.615 2082 Planarity : 0.006 0.064 2424 Dihedral : 7.484 34.422 1820 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.13 % Allowed : 1.06 % Favored : 98.80 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.94 (0.19), residues: 1682 helix: -1.94 (0.14), residues: 918 sheet: -0.37 (0.89), residues: 24 loop : -1.87 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 493 TYR 0.023 0.002 TYR A 740 PHE 0.018 0.002 PHE B 666 TRP 0.017 0.002 TRP B 600 HIS 0.010 0.002 HIS B 279 Details of bonding type rmsd covalent geometry : bond 0.00348 (13718) covalent geometry : angle 0.80194 (18604) hydrogen bonds : bond 0.06417 ( 602) hydrogen bonds : angle 6.76416 ( 1728) *********************** 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 96 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 243 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8491 (mt-10) REVERT: B 500 ASP cc_start: 0.8139 (t0) cc_final: 0.7857 (t70) REVERT: B 762 GLN cc_start: 0.8557 (mt0) cc_final: 0.7968 (tm-30) REVERT: B 766 MET cc_start: 0.8501 (ttm) cc_final: 0.8276 (ttm) outliers start: 1 outliers final: 1 residues processed: 96 average time/residue: 0.1582 time to fit residues: 20.5610 Evaluate side-chains 79 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 150 optimal weight: 9.9990 chunk 15 optimal weight: 0.0170 chunk 95 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 chunk 74 optimal weight: 0.0020 chunk 56 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 overall best weight: 0.4626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 GLN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.088892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.068940 restraints weight = 106408.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.071859 restraints weight = 57729.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.073636 restraints weight = 37707.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.074963 restraints weight = 28170.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.075692 restraints weight = 22701.868| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 13718 Z= 0.130 Angle : 0.708 11.354 18604 Z= 0.379 Chirality : 0.117 1.660 2082 Planarity : 0.005 0.063 2424 Dihedral : 6.573 28.090 1820 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.10 (0.18), residues: 1682 helix: -1.79 (0.14), residues: 942 sheet: -0.89 (0.80), residues: 24 loop : -2.35 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 585 TYR 0.019 0.001 TYR B 806 PHE 0.020 0.002 PHE B 666 TRP 0.011 0.001 TRP B 600 HIS 0.007 0.001 HIS B 279 Details of bonding type rmsd covalent geometry : bond 0.00292 (13718) covalent geometry : angle 0.70754 (18604) hydrogen bonds : bond 0.05029 ( 602) hydrogen bonds : angle 5.91058 ( 1728) *********************** 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 94 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.349 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: 0.8874 (mt-10) cc_final: 0.8581 (mt-10) REVERT: B 461 MET cc_start: 0.8197 (mmp) cc_final: 0.7911 (mmm) REVERT: B 500 ASP cc_start: 0.8230 (t0) cc_final: 0.7950 (t70) REVERT: B 762 GLN cc_start: 0.8575 (mt0) cc_final: 0.8270 (tm-30) REVERT: B 766 MET cc_start: 0.8476 (ttm) cc_final: 0.8260 (ttm) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1675 time to fit residues: 21.1492 Evaluate side-chains 79 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 2 optimal weight: 0.0980 chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 98 optimal weight: 0.0570 chunk 122 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.3700 ------------------------------------------------------------------------------- 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 697 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 = 0.3905 r_free = 0.3905 target = 0.088183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.068458 restraints weight = 107296.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.071159 restraints weight = 59029.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.072881 restraints weight = 38854.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.074125 restraints weight = 29144.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.074853 restraints weight = 23596.492| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 13718 Z= 0.155 Angle : 0.711 12.099 18604 Z= 0.379 Chirality : 0.118 1.681 2082 Planarity : 0.006 0.142 2424 Dihedral : 6.327 25.667 1820 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.13 % Allowed : 0.27 % Favored : 99.60 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.98 (0.18), residues: 1682 helix: -1.67 (0.14), residues: 930 sheet: -1.07 (0.70), residues: 24 loop : -2.34 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG B 13 TYR 0.015 0.001 TYR A 806 PHE 0.021 0.002 PHE A 666 TRP 0.010 0.001 TRP A 600 HIS 0.006 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00332 (13718) covalent geometry : angle 0.71070 (18604) hydrogen bonds : bond 0.04521 ( 602) hydrogen bonds : angle 5.69559 ( 1728) *********************** 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 86 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.305 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 243 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8560 (mt-10) REVERT: B 461 MET cc_start: 0.8376 (mmp) cc_final: 0.8053 (mmm) REVERT: B 500 ASP cc_start: 0.8238 (t0) cc_final: 0.8006 (t70) REVERT: B 762 GLN cc_start: 0.8579 (mt0) cc_final: 0.8331 (tm-30) REVERT: B 766 MET cc_start: 0.8495 (ttm) cc_final: 0.8289 (ttm) outliers start: 1 outliers final: 1 residues processed: 86 average time/residue: 0.1444 time to fit residues: 17.5095 Evaluate side-chains 76 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 159 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 550 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.088168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.068355 restraints weight = 107896.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.071159 restraints weight = 58580.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.072988 restraints weight = 38183.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.074172 restraints weight = 28315.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.074939 restraints weight = 22959.516| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13718 Z= 0.143 Angle : 0.681 11.213 18604 Z= 0.366 Chirality : 0.118 1.684 2082 Planarity : 0.005 0.064 2424 Dihedral : 5.934 25.735 1820 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.88 (0.18), residues: 1682 helix: -1.47 (0.15), residues: 936 sheet: -1.45 (0.65), residues: 24 loop : -2.45 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 13 TYR 0.015 0.001 TYR B 740 PHE 0.024 0.002 PHE A 666 TRP 0.010 0.001 TRP B 600 HIS 0.005 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00301 (13718) covalent geometry : angle 0.68053 (18604) hydrogen bonds : bond 0.04010 ( 602) hydrogen bonds : angle 5.34672 ( 1728) *********************** 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 86 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.381 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 243 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8529 (mt-10) REVERT: B 461 MET cc_start: 0.8429 (mmp) cc_final: 0.8128 (mmm) REVERT: B 500 ASP cc_start: 0.8293 (t0) cc_final: 0.8020 (t70) REVERT: B 762 GLN cc_start: 0.8591 (mt0) cc_final: 0.8319 (tm-30) REVERT: B 766 MET cc_start: 0.8499 (ttm) cc_final: 0.8298 (ttm) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1088 time to fit residues: 13.4647 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 : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 65 optimal weight: 0.0970 chunk 164 optimal weight: 0.0070 chunk 67 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 27 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.089177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.069371 restraints weight = 106766.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.072186 restraints weight = 57583.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.073988 restraints weight = 37848.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.075226 restraints weight = 28218.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.076011 restraints weight = 22990.076| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4702 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= 0.105 Angle : 0.646 11.377 18604 Z= 0.344 Chirality : 0.118 1.685 2082 Planarity : 0.004 0.063 2424 Dihedral : 5.622 24.147 1820 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.68 (0.18), residues: 1682 helix: -1.25 (0.15), residues: 956 sheet: -1.40 (0.67), residues: 24 loop : -2.48 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 13 TYR 0.015 0.001 TYR B 740 PHE 0.021 0.002 PHE A 666 TRP 0.025 0.001 TRP B 600 HIS 0.008 0.001 HIS A 900 Details of bonding type rmsd covalent geometry : bond 0.00232 (13718) covalent geometry : angle 0.64554 (18604) hydrogen bonds : bond 0.03734 ( 602) hydrogen bonds : angle 5.06823 ( 1728) *********************** 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 85 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.392 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: 0.8840 (mt-10) cc_final: 0.8510 (mt-10) REVERT: B 461 MET cc_start: 0.8404 (mmp) cc_final: 0.8032 (mmm) REVERT: B 500 ASP cc_start: 0.8222 (t0) cc_final: 0.7933 (t70) REVERT: B 762 GLN cc_start: 0.8589 (mt0) cc_final: 0.8331 (tm-30) REVERT: B 766 MET cc_start: 0.8516 (ttm) cc_final: 0.8287 (ttm) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1239 time to fit residues: 15.3972 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 : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 104 optimal weight: 0.6980 chunk 167 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 2 optimal weight: 0.0370 chunk 130 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 overall best weight: 1.0462 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.088570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.068845 restraints weight = 106738.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.071697 restraints weight = 58184.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.073458 restraints weight = 37765.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.074717 restraints weight = 28142.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.075512 restraints weight = 22776.120| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13718 Z= 0.124 Angle : 0.652 11.253 18604 Z= 0.348 Chirality : 0.116 1.689 2082 Planarity : 0.004 0.063 2424 Dihedral : 5.429 23.118 1820 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.18), residues: 1682 helix: -1.10 (0.15), residues: 946 sheet: -1.38 (0.71), residues: 24 loop : -2.41 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 13 TYR 0.016 0.001 TYR B 740 PHE 0.018 0.002 PHE B 666 TRP 0.011 0.001 TRP B 600 HIS 0.005 0.001 HIS A 900 Details of bonding type rmsd covalent geometry : bond 0.00269 (13718) covalent geometry : angle 0.65169 (18604) hydrogen bonds : bond 0.03635 ( 602) hydrogen bonds : angle 5.01940 ( 1728) *********************** 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 83 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 LEU cc_start: 0.8856 (tp) cc_final: 0.8623 (tp) REVERT: B 243 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8496 (mt-10) REVERT: B 461 MET cc_start: 0.8388 (mmp) cc_final: 0.8089 (mmm) REVERT: B 500 ASP cc_start: 0.8272 (t0) cc_final: 0.8000 (t70) REVERT: B 762 GLN cc_start: 0.8585 (mt0) cc_final: 0.8302 (tm-30) REVERT: B 766 MET cc_start: 0.8530 (ttm) cc_final: 0.8301 (ttm) REVERT: B 813 ILE cc_start: 0.5979 (mt) cc_final: 0.5777 (mt) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1051 time to fit residues: 12.9999 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 : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 105 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 164 optimal weight: 0.7980 chunk 127 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 0.0370 chunk 114 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.089134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.069506 restraints weight = 107127.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.072124 restraints weight = 58135.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.074025 restraints weight = 38833.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.075279 restraints weight = 28682.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.076126 restraints weight = 23175.331| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5122 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= 0.100 Angle : 0.630 11.412 18604 Z= 0.334 Chirality : 0.118 1.690 2082 Planarity : 0.004 0.063 2424 Dihedral : 5.236 22.395 1820 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.19), residues: 1682 helix: -0.79 (0.16), residues: 928 sheet: -1.41 (0.77), residues: 24 loop : -2.33 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 13 TYR 0.011 0.001 TYR B 806 PHE 0.022 0.001 PHE A 666 TRP 0.009 0.001 TRP A 530 HIS 0.005 0.001 HIS B 900 Details of bonding type rmsd covalent geometry : bond 0.00223 (13718) covalent geometry : angle 0.63016 (18604) hydrogen bonds : bond 0.03482 ( 602) hydrogen bonds : angle 4.87316 ( 1728) *********************** 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 89 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.376 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: A 243 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8473 (mp0) REVERT: A 288 TYR cc_start: 0.7124 (t80) cc_final: 0.6918 (t80) REVERT: A 461 MET cc_start: 0.8477 (mmp) cc_final: 0.8147 (mmm) REVERT: A 500 ASP cc_start: 0.8237 (t0) cc_final: 0.7954 (t70) REVERT: A 762 GLN cc_start: 0.8651 (mt0) cc_final: 0.8239 (tm-30) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1090 time to fit residues: 14.5848 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 : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 48 optimal weight: 0.1980 chunk 105 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 56 optimal weight: 8.9990 chunk 120 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.088901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.069375 restraints weight = 107668.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.072204 restraints weight = 57796.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.074061 restraints weight = 37695.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.075285 restraints weight = 27849.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.076104 restraints weight = 22491.376| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.5340 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= 0.101 Angle : 0.631 11.699 18604 Z= 0.335 Chirality : 0.120 1.714 2082 Planarity : 0.004 0.062 2424 Dihedral : 5.084 21.972 1820 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.19), residues: 1682 helix: -0.70 (0.16), residues: 930 sheet: -1.66 (0.80), residues: 24 loop : -2.34 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 13 TYR 0.011 0.001 TYR B 806 PHE 0.018 0.002 PHE B 666 TRP 0.009 0.001 TRP A 530 HIS 0.005 0.001 HIS B 900 Details of bonding type rmsd covalent geometry : bond 0.00223 (13718) covalent geometry : angle 0.63107 (18604) hydrogen bonds : bond 0.03388 ( 602) hydrogen bonds : angle 4.82056 ( 1728) *********************** 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 79 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.278 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: 0.8849 (tp) cc_final: 0.8636 (tp) REVERT: B 461 MET cc_start: 0.8397 (mmp) cc_final: 0.7947 (mmm) REVERT: B 500 ASP cc_start: 0.8278 (t0) cc_final: 0.7988 (t70) REVERT: B 762 GLN cc_start: 0.8529 (mt0) cc_final: 0.8283 (tm-30) REVERT: B 766 MET cc_start: 0.8589 (ttm) cc_final: 0.8372 (ttm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1105 time to fit residues: 13.1592 Evaluate side-chains 72 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 3 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.088733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.069098 restraints weight = 107386.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.071964 restraints weight = 58950.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.073827 restraints weight = 38468.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.075051 restraints weight = 28450.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.075848 restraints weight = 22977.149| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13718 Z= 0.109 Angle : 0.632 11.724 18604 Z= 0.334 Chirality : 0.120 1.703 2082 Planarity : 0.004 0.062 2424 Dihedral : 5.020 21.841 1820 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.19), residues: 1682 helix: -0.64 (0.16), residues: 932 sheet: -1.93 (0.79), residues: 24 loop : -2.32 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 13 TYR 0.011 0.001 TYR A 806 PHE 0.017 0.002 PHE B 666 TRP 0.008 0.001 TRP A 530 HIS 0.005 0.001 HIS B 900 Details of bonding type rmsd covalent geometry : bond 0.00242 (13718) covalent geometry : angle 0.63162 (18604) hydrogen bonds : bond 0.03326 ( 602) hydrogen bonds : angle 4.79936 ( 1728) ********************** 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 78 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 LEU cc_start: 0.8832 (tp) cc_final: 0.8566 (tp) REVERT: B 461 MET cc_start: 0.8377 (mmp) cc_final: 0.8052 (mmm) REVERT: B 500 ASP cc_start: 0.8222 (t0) cc_final: 0.7966 (t70) REVERT: B 762 GLN cc_start: 0.8508 (mt0) cc_final: 0.8261 (tm-30) REVERT: B 766 MET cc_start: 0.8576 (ttm) cc_final: 0.8365 (ttm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1188 time to fit residues: 14.0922 Evaluate side-chains 71 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 80 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 150 optimal weight: 0.2980 chunk 135 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.088736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.069041 restraints weight = 109012.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.071826 restraints weight = 59539.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.073544 restraints weight = 39129.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.074795 restraints weight = 29363.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.075581 restraints weight = 23926.978| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13718 Z= 0.116 Angle : 0.641 11.632 18604 Z= 0.339 Chirality : 0.120 1.705 2082 Planarity : 0.004 0.061 2424 Dihedral : 4.951 21.690 1820 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.19), residues: 1682 helix: -0.54 (0.16), residues: 930 sheet: -2.06 (0.76), residues: 24 loop : -2.36 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 13 TYR 0.010 0.001 TYR A 806 PHE 0.019 0.002 PHE A 666 TRP 0.008 0.001 TRP A 530 HIS 0.005 0.001 HIS B 900 Details of bonding type rmsd covalent geometry : bond 0.00255 (13718) covalent geometry : angle 0.64131 (18604) hydrogen bonds : bond 0.03255 ( 602) hydrogen bonds : angle 4.77867 ( 1728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2366.98 seconds wall clock time: 41 minutes 23.09 seconds (2483.09 seconds total)