Starting phenix.real_space_refine on Wed Mar 4 20:08:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7epd_31238/03_2026/7epd_31238.cif Found real_map, /net/cci-nas-00/data/ceres_data/7epd_31238/03_2026/7epd_31238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7epd_31238/03_2026/7epd_31238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7epd_31238/03_2026/7epd_31238.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7epd_31238/03_2026/7epd_31238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7epd_31238/03_2026/7epd_31238.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6655 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 6699 2.51 5 N 1925 2.21 5 O 2028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10710 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 5332 Classifications: {'peptide': 777} Incomplete info: {'truncation_to_alanine': 196} Link IDs: {'PTRANS': 37, 'TRANS': 739} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 756 Unresolved non-hydrogen angles: 978 Unresolved non-hydrogen dihedrals: 632 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 19, 'HIS:plan': 3, 'ASP:plan': 7, 'ASN:plan1': 6, 'GLN:plan1': 6, 'TYR:plan': 11, 'PHE:plan': 16, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 425 Chain: "B" Number of atoms: 5378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 5378 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 245} Link IDs: {'PTRANS': 37, 'TRANS': 754} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 901 Unresolved non-hydrogen angles: 1150 Unresolved non-hydrogen dihedrals: 733 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLU:plan': 18, 'GLN:plan1': 13, 'ASP:plan': 16, 'ARG:plan': 18, 'TYR:plan': 12, 'ASN:plan1': 9, 'PHE:plan': 16, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 483 Time building chain proxies: 2.14, per 1000 atoms: 0.20 Number of scatterers: 10710 At special positions: 0 Unit cell: (132.715, 118.085, 181.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 2028 8.00 N 1925 7.00 C 6699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 522 " distance=2.04 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 537 " distance=2.03 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS A 632 " - pdb=" SG CYS A 721 " distance=2.03 Simple disulfide: pdb=" SG CYS B 67 " - pdb=" SG CYS B 109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 249 " - pdb=" SG CYS B 541 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 437 " distance=2.03 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 545 " distance=2.03 Simple disulfide: pdb=" SG CYS B 548 " - pdb=" SG CYS B 560 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 655 " - pdb=" SG CYS B 749 " distance=2.03 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: 0.83 Conformation dependent library (CDL) restraints added in 588.8 milliseconds 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2922 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 47.6% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 59 through 74 Processing helix chain 'A' and resid 95 through 108 removed outlier: 4.164A pdb=" N ASP A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.930A pdb=" N LEU A 172 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 173 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP A 174 " --> pdb=" O LYS A 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 169 through 174' Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 190 through 202 removed outlier: 4.091A pdb=" N ALA A 194 " --> pdb=" O PHE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 232 Processing helix chain 'A' and resid 246 through 259 removed outlier: 3.771A pdb=" N PHE A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 285 removed outlier: 4.160A pdb=" N GLU A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 298 Processing helix chain 'A' and resid 324 through 333 Processing helix chain 'A' and resid 342 through 353 Processing helix chain 'A' and resid 377 through 400 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 564 through 592 removed outlier: 4.170A pdb=" N GLY A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Proline residue: A 571 - end of helix Processing helix chain 'A' and resid 595 through 600 Processing helix chain 'A' and resid 602 through 623 removed outlier: 3.577A pdb=" N TYR A 617 " --> pdb=" O VAL A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 661 removed outlier: 3.608A pdb=" N PHE A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 701 removed outlier: 3.793A pdb=" N CYS A 683 " --> pdb=" O GLN A 679 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 684 " --> pdb=" O VAL A 680 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY A 689 " --> pdb=" O ALA A 685 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 747 removed outlier: 3.976A pdb=" N GLY A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 783 Proline residue: A 778 - end of helix Processing helix chain 'A' and resid 784 through 786 No H-bonds generated for 'chain 'A' and resid 784 through 786' Processing helix chain 'A' and resid 788 through 817 removed outlier: 3.760A pdb=" N LEU A 809 " --> pdb=" O VAL A 805 " (cutoff:3.500A) Proline residue: A 812 - end of helix Processing helix chain 'B' and resid 72 through 77 Processing helix chain 'B' and resid 78 through 90 Processing helix chain 'B' and resid 113 through 128 removed outlier: 4.026A pdb=" N PHE B 122 " --> pdb=" O GLN B 118 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL B 123 " --> pdb=" O SER B 119 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 126 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 172 removed outlier: 4.105A pdb=" N ILE B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE B 168 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU B 171 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 removed outlier: 3.999A pdb=" N LEU B 186 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 229 through 245 removed outlier: 4.188A pdb=" N LYS B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU B 244 " --> pdb=" O GLN B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 277 removed outlier: 3.613A pdb=" N ASP B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG B 269 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 272 " --> pdb=" O ASP B 268 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 303 removed outlier: 3.787A pdb=" N GLN B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 350 Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.512A pdb=" N GLU B 369 " --> pdb=" O GLU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 3.639A pdb=" N LYS B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 430 removed outlier: 3.974A pdb=" N ILE B 412 " --> pdb=" O VAL B 408 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP B 413 " --> pdb=" O GLN B 409 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA B 414 " --> pdb=" O PHE B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 441 removed outlier: 3.525A pdb=" N GLU B 441 " --> pdb=" O PRO B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 454 removed outlier: 4.137A pdb=" N LEU B 448 " --> pdb=" O GLY B 444 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN B 454 " --> pdb=" O LYS B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 509 removed outlier: 4.403A pdb=" N MET B 509 " --> pdb=" O ILE B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 600 Processing helix chain 'B' and resid 600 through 613 removed outlier: 4.254A pdb=" N ALA B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE B 613 " --> pdb=" O MET B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.662A pdb=" N ARG B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 624 " --> pdb=" O ILE B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 646 removed outlier: 3.655A pdb=" N SER B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 630 " --> pdb=" O ARG B 626 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 659 Processing helix chain 'B' and resid 660 through 684 removed outlier: 3.545A pdb=" N GLY B 665 " --> pdb=" O PHE B 661 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET B 666 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 669 " --> pdb=" O GLY B 665 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR B 670 " --> pdb=" O MET B 666 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 671 " --> pdb=" O CYS B 667 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA B 672 " --> pdb=" O ILE B 668 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU B 673 " --> pdb=" O SER B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 722 Processing helix chain 'B' and resid 752 through 778 removed outlier: 4.420A pdb=" N TYR B 762 " --> pdb=" O CYS B 758 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N SER B 763 " --> pdb=" O SER B 759 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 765 " --> pdb=" O GLY B 761 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 809 Proline residue: B 806 - end of helix Processing helix chain 'B' and resid 816 through 819 Processing helix chain 'B' and resid 820 through 841 Processing helix chain 'B' and resid 841 through 850 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 3.526A pdb=" N ALA A 86 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 34 " --> pdb=" O HIS A 87 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU A 89 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLY A 36 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 238 through 241 removed outlier: 7.489A pdb=" N THR A 209 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL A 241 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA A 211 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 315 through 319 removed outlier: 6.352A pdb=" N TYR A 453 " --> pdb=" O TYR A 473 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TYR A 473 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE A 455 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG A 467 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 473 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 479 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 45 removed outlier: 3.757A pdb=" N ALA B 103 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 49 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ARG B 104 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU B 51 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU B 106 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLY B 53 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N THR B 50 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLY B 152 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 249 through 256 removed outlier: 5.633A pdb=" N VAL B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN B 252 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 225 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ALA B 282 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP B 310 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE B 336 " --> pdb=" O TRP B 310 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY B 312 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY B 496 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN B 481 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU B 494 " --> pdb=" O GLN B 481 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 553 through 555 removed outlier: 3.833A pdb=" N THR B 559 " --> pdb=" O PHE B 555 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1524 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: 1.77 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3704 1.34 - 1.46: 2459 1.46 - 1.58: 4681 1.58 - 1.70: 0 1.70 - 1.81: 75 Bond restraints: 10919 Sorted by residual: bond pdb=" C SER B 588 " pdb=" N PRO B 589 " ideal model delta sigma weight residual 1.335 1.344 -0.008 1.30e-02 5.92e+03 4.19e-01 bond pdb=" CA ILE B 518 " pdb=" C ILE B 518 " ideal model delta sigma weight residual 1.524 1.531 -0.007 1.05e-02 9.07e+03 4.03e-01 bond pdb=" C ARG A 411 " pdb=" N PRO A 412 " ideal model delta sigma weight residual 1.334 1.348 -0.014 2.34e-02 1.83e+03 3.73e-01 bond pdb=" C ALA A 710 " pdb=" N PRO A 711 " ideal model delta sigma weight residual 1.330 1.337 -0.007 1.22e-02 6.72e+03 3.63e-01 bond pdb=" CZ ARG A 183 " pdb=" NH2 ARG A 183 " ideal model delta sigma weight residual 1.330 1.322 0.008 1.30e-02 5.92e+03 3.41e-01 ... (remaining 10914 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 14599 1.24 - 2.48: 259 2.48 - 3.72: 59 3.72 - 4.96: 12 4.96 - 6.20: 7 Bond angle restraints: 14936 Sorted by residual: angle pdb=" N ILE B 722 " pdb=" CA ILE B 722 " pdb=" C ILE B 722 " ideal model delta sigma weight residual 112.98 110.05 2.93 1.25e+00 6.40e-01 5.48e+00 angle pdb=" N ILE B 518 " pdb=" CA ILE B 518 " pdb=" C ILE B 518 " ideal model delta sigma weight residual 108.88 113.85 -4.97 2.16e+00 2.14e-01 5.30e+00 angle pdb=" C PRO B 278 " pdb=" N ASN B 279 " pdb=" CA ASN B 279 " ideal model delta sigma weight residual 121.54 125.63 -4.09 1.91e+00 2.74e-01 4.58e+00 angle pdb=" CA ILE B 518 " pdb=" C ILE B 518 " pdb=" N PRO B 519 " ideal model delta sigma weight residual 118.88 122.15 -3.27 1.54e+00 4.22e-01 4.50e+00 angle pdb=" N GLY B 317 " pdb=" CA GLY B 317 " pdb=" C GLY B 317 " ideal model delta sigma weight residual 110.77 114.48 -3.71 1.93e+00 2.68e-01 3.70e+00 ... (remaining 14931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6036 17.91 - 35.81: 394 35.81 - 53.72: 58 53.72 - 71.63: 13 71.63 - 89.54: 7 Dihedral angle restraints: 6508 sinusoidal: 1986 harmonic: 4522 Sorted by residual: dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 92 " pdb=" CB CYS A 92 " ideal model delta sinusoidal sigma weight residual 93.00 11.26 81.74 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CB CYS A 504 " pdb=" SG CYS A 504 " pdb=" SG CYS A 522 " pdb=" CB CYS A 522 " ideal model delta sinusoidal sigma weight residual -86.00 -167.45 81.45 1 1.00e+01 1.00e-02 8.17e+01 dihedral pdb=" CB CYS A 632 " pdb=" SG CYS A 632 " pdb=" SG CYS A 721 " pdb=" CB CYS A 721 " ideal model delta sinusoidal sigma weight residual -86.00 -17.68 -68.32 1 1.00e+01 1.00e-02 6.05e+01 ... (remaining 6505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1059 0.029 - 0.059: 460 0.059 - 0.088: 136 0.088 - 0.117: 68 0.117 - 0.146: 10 Chirality restraints: 1733 Sorted by residual: chirality pdb=" CB ILE A 160 " pdb=" CA ILE A 160 " pdb=" CG1 ILE A 160 " pdb=" CG2 ILE A 160 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA ILE B 154 " pdb=" N ILE B 154 " pdb=" C ILE B 154 " pdb=" CB ILE B 154 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE A 485 " pdb=" N ILE A 485 " pdb=" C ILE A 485 " pdb=" CB ILE A 485 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1730 not shown) Planarity restraints: 1994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 720 " -0.010 2.00e-02 2.50e+03 1.00e-02 2.50e+00 pdb=" CG TRP B 720 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP B 720 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 720 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 720 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 720 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 720 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 720 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 720 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 720 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 739 " -0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO B 740 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 740 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 740 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 370 " 0.017 5.00e-02 4.00e+02 2.52e-02 1.02e+00 pdb=" N PRO A 371 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 371 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 371 " 0.014 5.00e-02 4.00e+02 ... (remaining 1991 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1950 2.77 - 3.30: 10441 3.30 - 3.83: 17804 3.83 - 4.37: 18655 4.37 - 4.90: 32519 Nonbonded interactions: 81369 Sorted by model distance: nonbonded pdb=" OG SER A 143 " pdb=" OH TYR A 165 " model vdw 2.232 3.040 nonbonded pdb=" O SER B 698 " pdb=" OG SER B 698 " model vdw 2.305 3.040 nonbonded pdb=" OG SER B 698 " pdb=" OG SER B 701 " model vdw 2.313 3.040 nonbonded pdb=" O TYR B 114 " pdb=" NE2 GLN B 118 " model vdw 2.319 3.120 nonbonded pdb=" NE2 GLN B 252 " pdb=" OE1 GLN B 273 " model vdw 2.349 3.120 ... (remaining 81364 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.600 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 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 : 0.002 0.020 10938 Z= 0.085 Angle : 0.448 6.199 14974 Z= 0.248 Chirality : 0.039 0.146 1733 Planarity : 0.003 0.036 1994 Dihedral : 12.271 89.537 3529 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.18), residues: 1557 helix: -0.34 (0.18), residues: 696 sheet: -2.45 (0.43), residues: 124 loop : -2.83 (0.18), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.008 0.001 TYR B 114 PHE 0.008 0.001 PHE A 189 TRP 0.027 0.001 TRP B 720 HIS 0.002 0.000 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00160 (10919) covalent geometry : angle 0.44777 (14936) SS BOND : bond 0.00175 ( 19) SS BOND : angle 0.57153 ( 38) hydrogen bonds : bond 0.15985 ( 519) hydrogen bonds : angle 5.40992 ( 1524) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8152 (tp) cc_final: 0.7948 (tt) REVERT: A 295 ASP cc_start: 0.7284 (t0) cc_final: 0.6712 (t0) REVERT: A 427 LYS cc_start: 0.5214 (tptp) cc_final: 0.4963 (mmmm) REVERT: B 170 ARG cc_start: 0.7112 (ttp-110) cc_final: 0.6863 (ttm170) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1174 time to fit residues: 22.6451 Evaluate side-chains 97 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.0670 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 393 HIS A 396 HIS A 439 ASN A 454 ASN B 98 ASN B 118 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS B 561 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.131381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.114241 restraints weight = 28171.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.112797 restraints weight = 52537.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.113682 restraints weight = 49819.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.113829 restraints weight = 29261.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.114220 restraints weight = 26197.082| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4020 r_free = 0.4020 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4020 r_free = 0.4020 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10938 Z= 0.117 Angle : 0.498 6.656 14974 Z= 0.256 Chirality : 0.040 0.147 1733 Planarity : 0.003 0.043 1994 Dihedral : 3.182 15.838 1657 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.59 % Allowed : 12.12 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.20), residues: 1557 helix: 1.18 (0.19), residues: 702 sheet: -2.12 (0.44), residues: 129 loop : -2.43 (0.20), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 44 TYR 0.017 0.001 TYR B 114 PHE 0.019 0.001 PHE B 480 TRP 0.012 0.001 TRP B 720 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00267 (10919) covalent geometry : angle 0.49690 (14936) SS BOND : bond 0.00195 ( 19) SS BOND : angle 0.90734 ( 38) hydrogen bonds : bond 0.02803 ( 519) hydrogen bonds : angle 3.76708 ( 1524) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.328 Fit side-chains REVERT: A 295 ASP cc_start: 0.7438 (t0) cc_final: 0.6741 (t0) REVERT: A 466 TYR cc_start: 0.5793 (m-80) cc_final: 0.5197 (m-80) REVERT: B 418 MET cc_start: 0.8381 (mtp) cc_final: 0.8090 (mtp) REVERT: B 738 MET cc_start: 0.2776 (pmm) cc_final: 0.2509 (ptp) outliers start: 14 outliers final: 8 residues processed: 116 average time/residue: 0.0851 time to fit residues: 15.0625 Evaluate side-chains 101 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 484 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 107 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 33 optimal weight: 0.5980 chunk 38 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 137 optimal weight: 40.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.129314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.108904 restraints weight = 27648.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.108789 restraints weight = 36171.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.107619 restraints weight = 26236.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.106533 restraints weight = 25474.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.106595 restraints weight = 27821.604| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10938 Z= 0.124 Angle : 0.484 6.141 14974 Z= 0.249 Chirality : 0.040 0.136 1733 Planarity : 0.003 0.041 1994 Dihedral : 3.228 18.247 1657 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.70 % Allowed : 15.74 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.21), residues: 1557 helix: 1.74 (0.20), residues: 702 sheet: -2.31 (0.42), residues: 130 loop : -2.21 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 568 TYR 0.013 0.001 TYR B 433 PHE 0.011 0.001 PHE A 289 TRP 0.006 0.001 TRP B 218 HIS 0.002 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00290 (10919) covalent geometry : angle 0.48261 (14936) SS BOND : bond 0.00229 ( 19) SS BOND : angle 0.85540 ( 38) hydrogen bonds : bond 0.02734 ( 519) hydrogen bonds : angle 3.55526 ( 1524) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 147 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8233 (t) REVERT: A 295 ASP cc_start: 0.7595 (t0) cc_final: 0.6995 (t0) REVERT: A 466 TYR cc_start: 0.6125 (m-80) cc_final: 0.5844 (m-80) REVERT: B 418 MET cc_start: 0.8484 (mtp) cc_final: 0.8232 (tpp) REVERT: B 738 MET cc_start: 0.2989 (pmm) cc_final: 0.2725 (ptp) outliers start: 15 outliers final: 10 residues processed: 107 average time/residue: 0.0830 time to fit residues: 13.6527 Evaluate side-chains 101 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 555 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 92 optimal weight: 0.0970 chunk 55 optimal weight: 50.0000 chunk 116 optimal weight: 0.2980 chunk 125 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 46 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.134244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.105144 restraints weight = 27150.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.104950 restraints weight = 24309.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.104721 restraints weight = 24677.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.104816 restraints weight = 22912.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.104873 restraints weight = 22049.798| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10938 Z= 0.135 Angle : 0.490 6.805 14974 Z= 0.251 Chirality : 0.040 0.136 1733 Planarity : 0.003 0.043 1994 Dihedral : 3.306 17.207 1657 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.60 % Allowed : 18.01 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.21), residues: 1557 helix: 1.98 (0.20), residues: 706 sheet: -2.43 (0.41), residues: 130 loop : -2.10 (0.21), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 568 TYR 0.009 0.001 TYR B 179 PHE 0.013 0.001 PHE A 289 TRP 0.008 0.001 TRP B 218 HIS 0.005 0.001 HIS B 424 Details of bonding type rmsd covalent geometry : bond 0.00319 (10919) covalent geometry : angle 0.48868 (14936) SS BOND : bond 0.00438 ( 19) SS BOND : angle 0.79306 ( 38) hydrogen bonds : bond 0.02593 ( 519) hydrogen bonds : angle 3.45565 ( 1524) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 295 ASP cc_start: 0.7600 (t0) cc_final: 0.6951 (t0) REVERT: A 466 TYR cc_start: 0.6152 (m-80) cc_final: 0.5400 (m-80) REVERT: B 440 MET cc_start: 0.7454 (mmm) cc_final: 0.6610 (mmt) REVERT: B 518 ILE cc_start: 0.5382 (OUTLIER) cc_final: 0.5119 (pt) outliers start: 23 outliers final: 17 residues processed: 114 average time/residue: 0.0806 time to fit residues: 14.1444 Evaluate side-chains 104 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 483 GLN Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 555 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 73 optimal weight: 30.0000 chunk 146 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.3980 chunk 117 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 53 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.0980 chunk 35 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.134387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3706 r_free = 0.3706 target = 0.104176 restraints weight = 26974.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.103997 restraints weight = 25994.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.104029 restraints weight = 25477.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.104058 restraints weight = 24999.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.104086 restraints weight = 23816.725| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10938 Z= 0.121 Angle : 0.481 6.717 14974 Z= 0.245 Chirality : 0.040 0.134 1733 Planarity : 0.003 0.040 1994 Dihedral : 3.297 18.485 1657 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.83 % Allowed : 18.69 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.22), residues: 1557 helix: 2.12 (0.20), residues: 707 sheet: -2.60 (0.42), residues: 125 loop : -2.02 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 568 TYR 0.012 0.001 TYR B 84 PHE 0.013 0.001 PHE A 105 TRP 0.007 0.001 TRP B 218 HIS 0.006 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00288 (10919) covalent geometry : angle 0.48010 (14936) SS BOND : bond 0.00197 ( 19) SS BOND : angle 0.78216 ( 38) hydrogen bonds : bond 0.02517 ( 519) hydrogen bonds : angle 3.40006 ( 1524) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 147 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8552 (t) REVERT: A 295 ASP cc_start: 0.7538 (t0) cc_final: 0.6931 (t0) REVERT: A 466 TYR cc_start: 0.6088 (m-80) cc_final: 0.5474 (m-80) REVERT: B 440 MET cc_start: 0.7440 (mmm) cc_final: 0.6585 (mmt) REVERT: B 518 ILE cc_start: 0.5468 (OUTLIER) cc_final: 0.5197 (pt) outliers start: 25 outliers final: 19 residues processed: 115 average time/residue: 0.0805 time to fit residues: 13.9982 Evaluate side-chains 108 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 483 GLN Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 555 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 87 optimal weight: 0.6980 chunk 10 optimal weight: 0.0570 chunk 43 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 153 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.133893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.111551 restraints weight = 27048.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.105285 restraints weight = 35002.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.104732 restraints weight = 34344.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.104641 restraints weight = 32085.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.105059 restraints weight = 28009.717| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10938 Z= 0.115 Angle : 0.476 6.561 14974 Z= 0.243 Chirality : 0.039 0.128 1733 Planarity : 0.003 0.040 1994 Dihedral : 3.287 17.875 1657 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.17 % Allowed : 18.91 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.22), residues: 1557 helix: 2.11 (0.20), residues: 719 sheet: -2.54 (0.43), residues: 131 loop : -1.96 (0.21), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 568 TYR 0.013 0.001 TYR B 84 PHE 0.014 0.001 PHE A 105 TRP 0.007 0.001 TRP B 218 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00271 (10919) covalent geometry : angle 0.47518 (14936) SS BOND : bond 0.00203 ( 19) SS BOND : angle 0.75063 ( 38) hydrogen bonds : bond 0.02450 ( 519) hydrogen bonds : angle 3.34593 ( 1524) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 147 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8415 (t) REVERT: A 225 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7456 (mm-30) REVERT: A 291 TRP cc_start: 0.7877 (p90) cc_final: 0.7126 (p90) REVERT: A 295 ASP cc_start: 0.7312 (t0) cc_final: 0.6647 (t0) REVERT: A 466 TYR cc_start: 0.6300 (m-80) cc_final: 0.5703 (m-80) REVERT: B 440 MET cc_start: 0.7538 (mmm) cc_final: 0.6692 (mmt) REVERT: B 518 ILE cc_start: 0.5573 (OUTLIER) cc_final: 0.5318 (pt) outliers start: 28 outliers final: 21 residues processed: 115 average time/residue: 0.0792 time to fit residues: 14.1472 Evaluate side-chains 112 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 555 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 112 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 30.0000 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.135815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.101394 restraints weight = 26423.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.101778 restraints weight = 24869.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.101550 restraints weight = 23907.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.101676 restraints weight = 21343.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.101702 restraints weight = 20683.036| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10938 Z= 0.162 Angle : 0.513 7.036 14974 Z= 0.263 Chirality : 0.040 0.154 1733 Planarity : 0.003 0.044 1994 Dihedral : 3.522 20.964 1657 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.85 % Allowed : 18.57 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.22), residues: 1557 helix: 2.12 (0.20), residues: 719 sheet: -2.41 (0.44), residues: 128 loop : -1.93 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 568 TYR 0.016 0.001 TYR B 84 PHE 0.015 0.001 PHE B 172 TRP 0.010 0.001 TRP B 218 HIS 0.004 0.001 HIS B 423 Details of bonding type rmsd covalent geometry : bond 0.00387 (10919) covalent geometry : angle 0.51190 (14936) SS BOND : bond 0.00251 ( 19) SS BOND : angle 0.83412 ( 38) hydrogen bonds : bond 0.02713 ( 519) hydrogen bonds : angle 3.45139 ( 1524) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 147 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8486 (t) REVERT: A 291 TRP cc_start: 0.7850 (p90) cc_final: 0.7631 (p90) REVERT: A 295 ASP cc_start: 0.7446 (t0) cc_final: 0.6791 (t0) REVERT: A 466 TYR cc_start: 0.6719 (m-80) cc_final: 0.6180 (m-80) REVERT: B 440 MET cc_start: 0.7537 (mmm) cc_final: 0.7125 (mmt) REVERT: B 518 ILE cc_start: 0.5797 (OUTLIER) cc_final: 0.5549 (pt) outliers start: 34 outliers final: 22 residues processed: 119 average time/residue: 0.0854 time to fit residues: 15.4124 Evaluate side-chains 113 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 555 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 116 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 134 optimal weight: 0.3980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.136330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.106286 restraints weight = 27071.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.103300 restraints weight = 22872.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.104190 restraints weight = 25706.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.104173 restraints weight = 23653.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.104356 restraints weight = 21297.874| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10938 Z= 0.169 Angle : 0.539 9.891 14974 Z= 0.276 Chirality : 0.041 0.167 1733 Planarity : 0.004 0.045 1994 Dihedral : 3.661 21.768 1657 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.74 % Allowed : 19.82 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.22), residues: 1557 helix: 2.11 (0.20), residues: 719 sheet: -2.57 (0.42), residues: 138 loop : -1.86 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 231 TYR 0.017 0.001 TYR B 84 PHE 0.013 0.001 PHE A 289 TRP 0.016 0.001 TRP B 218 HIS 0.003 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00405 (10919) covalent geometry : angle 0.53728 (14936) SS BOND : bond 0.00255 ( 19) SS BOND : angle 0.98529 ( 38) hydrogen bonds : bond 0.02724 ( 519) hydrogen bonds : angle 3.50993 ( 1524) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 225 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7353 (mm-30) REVERT: A 259 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7237 (mt0) REVERT: A 295 ASP cc_start: 0.7476 (t0) cc_final: 0.6716 (t0) REVERT: A 466 TYR cc_start: 0.6771 (m-80) cc_final: 0.6270 (m-80) REVERT: A 504 CYS cc_start: 0.3826 (OUTLIER) cc_final: 0.3606 (p) REVERT: B 440 MET cc_start: 0.7736 (mmm) cc_final: 0.7343 (mmt) REVERT: B 518 ILE cc_start: 0.6099 (OUTLIER) cc_final: 0.5853 (pt) outliers start: 33 outliers final: 28 residues processed: 122 average time/residue: 0.0773 time to fit residues: 14.6491 Evaluate side-chains 117 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 555 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 36 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 76 optimal weight: 40.0000 chunk 122 optimal weight: 0.5980 chunk 63 optimal weight: 40.0000 chunk 113 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 144 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.134922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.099808 restraints weight = 26426.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.100258 restraints weight = 24233.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.100436 restraints weight = 20880.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.100290 restraints weight = 22385.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.100406 restraints weight = 20685.196| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10938 Z= 0.160 Angle : 0.547 10.610 14974 Z= 0.278 Chirality : 0.041 0.163 1733 Planarity : 0.004 0.047 1994 Dihedral : 3.689 22.045 1657 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.30 % Allowed : 19.59 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.22), residues: 1557 helix: 2.11 (0.20), residues: 725 sheet: -2.60 (0.44), residues: 131 loop : -1.91 (0.21), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 568 TYR 0.018 0.001 TYR B 84 PHE 0.012 0.001 PHE B 172 TRP 0.014 0.001 TRP B 218 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00384 (10919) covalent geometry : angle 0.54304 (14936) SS BOND : bond 0.00301 ( 19) SS BOND : angle 1.36559 ( 38) hydrogen bonds : bond 0.02694 ( 519) hydrogen bonds : angle 3.48958 ( 1524) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 89 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 295 ASP cc_start: 0.7370 (t0) cc_final: 0.6660 (t0) REVERT: A 466 TYR cc_start: 0.6732 (m-80) cc_final: 0.6217 (m-80) REVERT: B 366 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: B 425 MET cc_start: 0.7383 (mtt) cc_final: 0.7106 (mtt) REVERT: B 440 MET cc_start: 0.7832 (mmm) cc_final: 0.7321 (mmt) REVERT: B 518 ILE cc_start: 0.6094 (OUTLIER) cc_final: 0.5852 (pt) outliers start: 38 outliers final: 29 residues processed: 122 average time/residue: 0.0823 time to fit residues: 15.5701 Evaluate side-chains 118 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 555 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 132 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 91 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.136878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.106127 restraints weight = 27342.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.104975 restraints weight = 21408.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.104548 restraints weight = 20906.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.104794 restraints weight = 24018.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.104810 restraints weight = 22218.496| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10938 Z= 0.127 Angle : 0.531 10.188 14974 Z= 0.268 Chirality : 0.040 0.170 1733 Planarity : 0.003 0.047 1994 Dihedral : 3.652 21.767 1657 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.51 % Allowed : 20.16 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.22), residues: 1557 helix: 2.13 (0.20), residues: 725 sheet: -2.54 (0.45), residues: 131 loop : -1.89 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 231 TYR 0.018 0.001 TYR B 84 PHE 0.013 0.001 PHE A 105 TRP 0.015 0.001 TRP B 218 HIS 0.005 0.001 HIS B 735 Details of bonding type rmsd covalent geometry : bond 0.00301 (10919) covalent geometry : angle 0.52794 (14936) SS BOND : bond 0.00387 ( 19) SS BOND : angle 1.22661 ( 38) hydrogen bonds : bond 0.02563 ( 519) hydrogen bonds : angle 3.42457 ( 1524) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 225 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7299 (mm-30) REVERT: A 259 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7274 (mt0) REVERT: A 295 ASP cc_start: 0.7337 (t0) cc_final: 0.6687 (t0) REVERT: A 466 TYR cc_start: 0.6652 (m-80) cc_final: 0.6138 (m-80) REVERT: B 366 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: B 425 MET cc_start: 0.7323 (mtt) cc_final: 0.7074 (mtt) REVERT: B 440 MET cc_start: 0.7895 (mmm) cc_final: 0.7411 (mmt) REVERT: B 518 ILE cc_start: 0.6071 (OUTLIER) cc_final: 0.5822 (pt) outliers start: 31 outliers final: 26 residues processed: 116 average time/residue: 0.0795 time to fit residues: 14.1138 Evaluate side-chains 114 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 555 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 67 optimal weight: 0.0000 chunk 46 optimal weight: 0.5980 chunk 130 optimal weight: 0.0670 chunk 142 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 85 optimal weight: 0.4980 overall best weight: 0.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.136534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.101444 restraints weight = 26699.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.102502 restraints weight = 24841.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.102658 restraints weight = 21614.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.102762 restraints weight = 19716.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.102805 restraints weight = 20177.652| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10938 Z= 0.104 Angle : 0.514 9.281 14974 Z= 0.259 Chirality : 0.040 0.139 1733 Planarity : 0.003 0.046 1994 Dihedral : 3.502 20.433 1657 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.06 % Allowed : 20.95 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.22), residues: 1557 helix: 2.20 (0.20), residues: 722 sheet: -2.48 (0.45), residues: 131 loop : -1.86 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 568 TYR 0.016 0.001 TYR B 84 PHE 0.012 0.001 PHE A 105 TRP 0.022 0.001 TRP A 291 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00240 (10919) covalent geometry : angle 0.51199 (14936) SS BOND : bond 0.00355 ( 19) SS BOND : angle 1.01123 ( 38) hydrogen bonds : bond 0.02419 ( 519) hydrogen bonds : angle 3.34619 ( 1524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1872.86 seconds wall clock time: 32 minutes 49.51 seconds (1969.51 seconds total)