Starting phenix.real_space_refine on Tue Dec 31 15:49:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7epd_31238/12_2024/7epd_31238.cif Found real_map, /net/cci-nas-00/data/ceres_data/7epd_31238/12_2024/7epd_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7epd_31238/12_2024/7epd_31238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7epd_31238/12_2024/7epd_31238.map" model { file = "/net/cci-nas-00/data/ceres_data/7epd_31238/12_2024/7epd_31238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7epd_31238/12_2024/7epd_31238.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 11, 'ASN:plan1': 6, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 16, 'GLU:plan': 13, 'ARG:plan': 19} 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: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 16, 'PHE:plan': 16, 'GLU:plan': 18, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 483 Time building chain proxies: 6.22, per 1000 atoms: 0.58 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: 2.64 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.10 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: 3.10 Time building geometry restraints manager: 3.09 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 26.120 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.440 ------------------------------------------------------------------------------- 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 10919 Z= 0.106 Angle : 0.448 6.199 14936 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (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 TRP 0.027 0.001 TRP B 720 HIS 0.002 0.000 HIS A 119 PHE 0.008 0.001 PHE A 189 TYR 0.008 0.001 TYR B 114 ARG 0.002 0.000 ARG A 183 *********************** 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 : 1.324 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: 0.6864 (ttm170) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2545 time to fit residues: 49.8167 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 : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 79 optimal weight: 10.0000 chunk 63 optimal weight: 50.0000 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 74 optimal weight: 40.0000 chunk 91 optimal weight: 0.9990 chunk 141 optimal weight: 9.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10919 Z= 0.335 Angle : 0.577 6.991 14936 Z= 0.300 Chirality : 0.043 0.171 1733 Planarity : 0.004 0.045 1994 Dihedral : 3.551 17.420 1657 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.81 % Allowed : 14.04 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.21), residues: 1557 helix: 1.07 (0.19), residues: 707 sheet: -2.35 (0.43), residues: 137 loop : -2.37 (0.20), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 218 HIS 0.005 0.001 HIS A 41 PHE 0.021 0.002 PHE A 289 TYR 0.018 0.001 TYR B 114 ARG 0.007 0.001 ARG B 44 *********************** 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 119 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 295 ASP cc_start: 0.7817 (t0) cc_final: 0.7178 (t0) REVERT: A 427 LYS cc_start: 0.6132 (tptp) cc_final: 0.5514 (tptp) REVERT: A 466 TYR cc_start: 0.6239 (m-80) cc_final: 0.5762 (m-80) REVERT: B 738 MET cc_start: 0.2816 (pmm) cc_final: 0.2487 (ptp) outliers start: 16 outliers final: 13 residues processed: 113 average time/residue: 0.2183 time to fit residues: 36.4463 Evaluate side-chains 99 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 271 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 483 GLN Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 499 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 126 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 chunk 48 optimal weight: 0.0670 chunk 113 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10919 Z= 0.185 Angle : 0.482 6.025 14936 Z= 0.248 Chirality : 0.040 0.142 1733 Planarity : 0.003 0.040 1994 Dihedral : 3.368 19.678 1657 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.83 % Allowed : 16.08 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.21), residues: 1557 helix: 1.69 (0.20), residues: 703 sheet: -2.39 (0.41), residues: 137 loop : -2.23 (0.20), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 218 HIS 0.003 0.001 HIS A 56 PHE 0.010 0.001 PHE A 289 TYR 0.014 0.001 TYR B 84 ARG 0.008 0.000 ARG B 568 *********************** 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 123 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: A 147 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8185 (t) REVERT: A 295 ASP cc_start: 0.7812 (t0) cc_final: 0.7171 (t0) REVERT: A 427 LYS cc_start: 0.5973 (tptp) cc_final: 0.5542 (tptp) REVERT: A 466 TYR cc_start: 0.5977 (m-80) cc_final: 0.5204 (m-80) REVERT: B 358 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.7409 (t0) REVERT: B 738 MET cc_start: 0.3038 (pmm) cc_final: 0.2517 (ptp) outliers start: 25 outliers final: 16 residues processed: 114 average time/residue: 0.2067 time to fit residues: 35.2108 Evaluate side-chains 105 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 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 358 ASN 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 509 MET 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 140 optimal weight: 9.9990 chunk 106 optimal weight: 0.5980 chunk 73 optimal weight: 30.0000 chunk 15 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 150 optimal weight: 20.0000 chunk 74 optimal weight: 50.0000 chunk 134 optimal weight: 0.0020 chunk 40 optimal weight: 0.4980 overall best weight: 0.9190 ------------------------------------------------------------------------------- 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 252 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** B 587 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10919 Z= 0.262 Angle : 0.510 6.456 14936 Z= 0.262 Chirality : 0.040 0.152 1733 Planarity : 0.003 0.043 1994 Dihedral : 3.518 19.379 1657 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.94 % Allowed : 17.78 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.22), residues: 1557 helix: 1.87 (0.20), residues: 709 sheet: -2.54 (0.42), residues: 132 loop : -2.08 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 218 HIS 0.004 0.001 HIS A 56 PHE 0.014 0.001 PHE A 289 TYR 0.012 0.001 TYR B 84 ARG 0.007 0.000 ARG B 568 *********************** 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 120 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 147 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8276 (t) REVERT: A 291 TRP cc_start: 0.7856 (p90) cc_final: 0.6855 (p90) REVERT: A 295 ASP cc_start: 0.7855 (t0) cc_final: 0.7258 (t0) REVERT: A 466 TYR cc_start: 0.6171 (m-80) cc_final: 0.5551 (m-80) REVERT: B 440 MET cc_start: 0.7513 (mmm) cc_final: 0.6694 (mmt) REVERT: B 518 ILE cc_start: 0.5200 (OUTLIER) cc_final: 0.4927 (pt) outliers start: 26 outliers final: 17 residues processed: 115 average time/residue: 0.2088 time to fit residues: 36.3469 Evaluate side-chains 109 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.0770 chunk 85 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 40.0000 chunk 128 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 30.0000 chunk 135 optimal weight: 40.0000 chunk 38 optimal weight: 1.9990 overall best weight: 1.5344 ------------------------------------------------------------------------------- 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 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** B 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 10919 Z= 0.401 Angle : 0.606 6.707 14936 Z= 0.315 Chirality : 0.043 0.244 1733 Planarity : 0.004 0.058 1994 Dihedral : 4.110 21.950 1657 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.44 % Allowed : 16.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.22), residues: 1557 helix: 1.83 (0.20), residues: 721 sheet: -2.56 (0.42), residues: 132 loop : -2.00 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 218 HIS 0.004 0.001 HIS B 423 PHE 0.019 0.002 PHE B 122 TYR 0.016 0.002 TYR B 367 ARG 0.010 0.001 ARG B 568 *********************** 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 142 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 94 time to evaluate : 1.242 Fit side-chains REVERT: A 225 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7400 (mm-30) REVERT: A 291 TRP cc_start: 0.7947 (p90) cc_final: 0.7538 (p90) REVERT: A 295 ASP cc_start: 0.7848 (t0) cc_final: 0.7176 (t0) REVERT: A 466 TYR cc_start: 0.6799 (m-80) cc_final: 0.6308 (m-80) REVERT: B 440 MET cc_start: 0.7632 (mmm) cc_final: 0.7140 (mmt) REVERT: B 465 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8910 (p) REVERT: B 518 ILE cc_start: 0.5835 (OUTLIER) cc_final: 0.5611 (pt) REVERT: B 558 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.6207 (tpp) REVERT: B 735 HIS cc_start: 0.5982 (OUTLIER) cc_final: 0.5229 (p-80) outliers start: 48 outliers final: 29 residues processed: 134 average time/residue: 0.1902 time to fit residues: 39.1826 Evaluate side-chains 121 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 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 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 334 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 362 VAL 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 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 Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 735 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 5.9990 chunk 135 optimal weight: 40.0000 chunk 29 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 125 optimal weight: 0.0570 chunk 69 optimal weight: 30.0000 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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** A 439 ASN B 205 GLN ** 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** B 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10919 Z= 0.212 Angle : 0.529 6.856 14936 Z= 0.272 Chirality : 0.040 0.146 1733 Planarity : 0.003 0.045 1994 Dihedral : 3.807 20.615 1657 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.19 % Allowed : 19.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.22), residues: 1557 helix: 1.91 (0.20), residues: 722 sheet: -2.58 (0.42), residues: 138 loop : -1.95 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 218 HIS 0.003 0.001 HIS A 390 PHE 0.012 0.001 PHE A 105 TYR 0.016 0.001 TYR B 84 ARG 0.005 0.000 ARG B 568 *********************** 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 130 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: A 259 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7102 (mt0) REVERT: A 291 TRP cc_start: 0.7962 (p90) cc_final: 0.7657 (p90) REVERT: A 295 ASP cc_start: 0.7535 (t0) cc_final: 0.6858 (t0) REVERT: A 466 TYR cc_start: 0.6579 (m-80) cc_final: 0.6195 (m-80) REVERT: B 186 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8307 (pp) REVERT: B 440 MET cc_start: 0.7656 (mmm) cc_final: 0.7145 (mmt) REVERT: B 483 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.7152 (mt0) REVERT: B 518 ILE cc_start: 0.5708 (OUTLIER) cc_final: 0.5478 (pt) outliers start: 37 outliers final: 26 residues processed: 125 average time/residue: 0.2022 time to fit residues: 38.5033 Evaluate side-chains 118 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 221 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 269 PHE 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 79 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 186 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 292 ILE Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 362 VAL 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 Chi-restraints excluded: chain B residue 558 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 0.1980 chunk 110 optimal weight: 0.0170 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 150 optimal weight: 40.0000 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 30.0000 chunk 93 optimal weight: 0.4980 overall best weight: 0.5422 ------------------------------------------------------------------------------- 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** A 439 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10919 Z= 0.190 Angle : 0.516 8.305 14936 Z= 0.264 Chirality : 0.040 0.136 1733 Planarity : 0.003 0.045 1994 Dihedral : 3.697 20.027 1657 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.08 % Allowed : 20.72 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.22), residues: 1557 helix: 2.00 (0.20), residues: 722 sheet: -2.50 (0.43), residues: 138 loop : -1.91 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 218 HIS 0.003 0.001 HIS A 390 PHE 0.013 0.001 PHE B 480 TYR 0.017 0.001 TYR B 482 ARG 0.004 0.000 ARG B 568 *********************** 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 127 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: A 225 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7346 (mm-30) REVERT: A 259 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7078 (mt0) REVERT: A 291 TRP cc_start: 0.7966 (p90) cc_final: 0.7758 (p90) REVERT: A 295 ASP cc_start: 0.7519 (t0) cc_final: 0.6888 (t0) REVERT: A 337 TRP cc_start: 0.6884 (OUTLIER) cc_final: 0.5699 (m100) REVERT: A 466 TYR cc_start: 0.6618 (m-80) cc_final: 0.6247 (m-80) REVERT: B 186 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8290 (pp) REVERT: B 440 MET cc_start: 0.7620 (mmm) cc_final: 0.7254 (mmt) REVERT: B 518 ILE cc_start: 0.5675 (OUTLIER) cc_final: 0.5456 (pt) outliers start: 36 outliers final: 24 residues processed: 123 average time/residue: 0.2268 time to fit residues: 40.7776 Evaluate side-chains 114 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 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 292 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 381 VAL 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 186 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 292 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 455 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 50.0000 chunk 89 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 102 optimal weight: 0.0470 chunk 74 optimal weight: 50.0000 chunk 14 optimal weight: 1.9990 chunk 118 optimal weight: 0.0770 chunk 136 optimal weight: 7.9990 chunk 144 optimal weight: 0.0170 overall best weight: 0.4276 ------------------------------------------------------------------------------- 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 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10919 Z= 0.163 Angle : 0.501 8.699 14936 Z= 0.256 Chirality : 0.039 0.131 1733 Planarity : 0.003 0.046 1994 Dihedral : 3.563 19.620 1657 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.96 % Allowed : 20.95 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.22), residues: 1557 helix: 2.07 (0.20), residues: 720 sheet: -2.55 (0.45), residues: 131 loop : -1.85 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 218 HIS 0.003 0.001 HIS A 56 PHE 0.011 0.001 PHE A 422 TYR 0.017 0.001 TYR B 84 ARG 0.005 0.000 ARG B 568 *********************** 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 128 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 225 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7372 (mm-30) REVERT: A 243 ARG cc_start: 0.6569 (mpp-170) cc_final: 0.5656 (mmt90) REVERT: A 259 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7166 (mt0) REVERT: A 295 ASP cc_start: 0.7448 (t0) cc_final: 0.6859 (t0) REVERT: A 337 TRP cc_start: 0.6946 (OUTLIER) cc_final: 0.5811 (m100) REVERT: A 466 TYR cc_start: 0.6646 (m-80) cc_final: 0.6272 (m-80) REVERT: B 186 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8267 (pp) REVERT: B 440 MET cc_start: 0.7786 (mmm) cc_final: 0.7268 (mmt) REVERT: B 518 ILE cc_start: 0.5574 (OUTLIER) cc_final: 0.5303 (pt) outliers start: 35 outliers final: 25 residues processed: 123 average time/residue: 0.2010 time to fit residues: 38.7085 Evaluate side-chains 116 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 1.283 ------------------------------------------------------------------------------- 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 221 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 186 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 292 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 455 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 Chi-restraints excluded: chain B residue 840 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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** ** A 390 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 10919 Z= 0.477 Angle : 0.643 8.624 14936 Z= 0.333 Chirality : 0.045 0.258 1733 Planarity : 0.004 0.051 1994 Dihedral : 4.183 22.468 1657 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.53 % Allowed : 20.72 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.22), residues: 1557 helix: 1.89 (0.20), residues: 733 sheet: -2.66 (0.44), residues: 120 loop : -1.93 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 218 HIS 0.004 0.001 HIS B 423 PHE 0.018 0.002 PHE B 238 TYR 0.023 0.002 TYR B 482 ARG 0.006 0.001 ARG B 568 *********************** 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 133 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 93 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: A 259 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7209 (mt0) REVERT: A 291 TRP cc_start: 0.7983 (OUTLIER) cc_final: 0.7780 (p90) REVERT: A 295 ASP cc_start: 0.7616 (t0) cc_final: 0.6965 (t0) REVERT: A 337 TRP cc_start: 0.7003 (OUTLIER) cc_final: 0.5862 (m100) REVERT: B 440 MET cc_start: 0.7900 (mmm) cc_final: 0.7365 (mmt) REVERT: B 518 ILE cc_start: 0.5804 (OUTLIER) cc_final: 0.5587 (pt) REVERT: B 738 MET cc_start: 0.2489 (ptp) cc_final: 0.1770 (ptp) outliers start: 40 outliers final: 30 residues processed: 129 average time/residue: 0.1809 time to fit residues: 36.3214 Evaluate side-chains 123 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 221 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 291 TRP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain B residue 79 LEU 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 362 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 430 CYS 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 148 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 40.0000 chunk 143 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 98 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** A 390 HIS A 396 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10919 Z= 0.219 Angle : 0.562 9.880 14936 Z= 0.287 Chirality : 0.043 0.568 1733 Planarity : 0.004 0.043 1994 Dihedral : 3.950 22.289 1657 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.08 % Allowed : 21.52 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.22), residues: 1557 helix: 2.00 (0.20), residues: 720 sheet: -2.49 (0.43), residues: 136 loop : -1.89 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 218 HIS 0.003 0.001 HIS A 56 PHE 0.015 0.001 PHE B 195 TYR 0.020 0.001 TYR B 84 ARG 0.004 0.000 ARG B 568 ********************** 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 125 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 89 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: A 225 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7251 (mm-30) REVERT: A 259 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7223 (mt0) REVERT: A 295 ASP cc_start: 0.7438 (t0) cc_final: 0.6869 (t0) REVERT: A 337 TRP cc_start: 0.6905 (OUTLIER) cc_final: 0.5835 (m100) REVERT: B 440 MET cc_start: 0.7916 (mmm) cc_final: 0.7413 (mmt) REVERT: B 518 ILE cc_start: 0.5655 (OUTLIER) cc_final: 0.5446 (pt) outliers start: 36 outliers final: 29 residues processed: 121 average time/residue: 0.1821 time to fit residues: 34.2600 Evaluate side-chains 121 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 221 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain B residue 79 LEU 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 249 CYS 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 430 CYS 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 131 optimal weight: 0.0470 chunk 37 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 123 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** 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 = 0.4209 r_free = 0.4209 target = 0.134466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.103077 restraints weight = 25785.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.102279 restraints weight = 22194.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.101739 restraints weight = 22715.866| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10919 Z= 0.207 Angle : 0.549 8.588 14936 Z= 0.280 Chirality : 0.041 0.369 1733 Planarity : 0.004 0.045 1994 Dihedral : 3.840 22.921 1657 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.08 % Allowed : 21.97 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.22), residues: 1557 helix: 2.05 (0.20), residues: 719 sheet: -2.45 (0.44), residues: 136 loop : -1.85 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 218 HIS 0.004 0.001 HIS A 390 PHE 0.013 0.001 PHE B 195 TYR 0.018 0.001 TYR B 84 ARG 0.004 0.000 ARG B 568 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2128.46 seconds wall clock time: 39 minutes 51.72 seconds (2391.72 seconds total)