Starting phenix.real_space_refine on Mon Jul 28 15:53:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7klv_22919/07_2025/7klv_22919.cif Found real_map, /net/cci-nas-00/data/ceres_data/7klv_22919/07_2025/7klv_22919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7klv_22919/07_2025/7klv_22919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7klv_22919/07_2025/7klv_22919.map" model { file = "/net/cci-nas-00/data/ceres_data/7klv_22919/07_2025/7klv_22919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7klv_22919/07_2025/7klv_22919.cif" } resolution = 3.1 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= 0.003 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 522 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 6 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 6233 2.51 5 N 1715 2.21 5 O 1869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9871 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4890 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 18, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 4915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4915 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 18, 'TRANS': 595} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.02, per 1000 atoms: 0.71 Number of scatterers: 9871 At special positions: 0 Unit cell: (121.378, 129.018, 90.8216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 S 44 16.00 P 6 15.00 Mg 2 11.99 O 1869 8.00 N 1715 7.00 C 6233 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2338 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 13 sheets defined 46.7% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 93 through 104 Processing helix chain 'A' and resid 110 through 135 removed outlier: 4.355A pdb=" N ARG A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 173 Processing helix chain 'A' and resid 178 through 186 removed outlier: 3.921A pdb=" N ALA A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 210 removed outlier: 3.505A pdb=" N SER A 207 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.527A pdb=" N PHE A 264 " --> pdb=" O CYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 307 through 319 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 408 through 433 Processing helix chain 'A' and resid 433 through 455 removed outlier: 3.545A pdb=" N LYS A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 466 removed outlier: 3.604A pdb=" N LYS A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 511 through 518 removed outlier: 3.698A pdb=" N ALA A 516 " --> pdb=" O PRO A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 540 Processing helix chain 'A' and resid 550 through 557 removed outlier: 3.940A pdb=" N VAL A 555 " --> pdb=" O GLU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 590 removed outlier: 4.313A pdb=" N GLU A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LEU A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 628 Processing helix chain 'A' and resid 648 through 658 removed outlier: 3.714A pdb=" N LEU A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN A 655 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLN A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 681 removed outlier: 3.885A pdb=" N LEU A 667 " --> pdb=" O GLY A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 688 removed outlier: 4.063A pdb=" N ALA A 688 " --> pdb=" O ASP A 685 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 685 through 688' Processing helix chain 'A' and resid 689 through 701 removed outlier: 3.960A pdb=" N LEU A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 Processing helix chain 'B' and resid 110 through 135 removed outlier: 4.300A pdb=" N ARG B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 178 through 186 removed outlier: 3.933A pdb=" N ALA B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 210 removed outlier: 3.557A pdb=" N SER B 207 " --> pdb=" O GLY B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 removed outlier: 3.598A pdb=" N PHE B 264 " --> pdb=" O CYS B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 307 through 320 Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 408 through 433 removed outlier: 3.648A pdb=" N ASP B 416 " --> pdb=" O ARG B 412 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER B 430 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS B 431 " --> pdb=" O ILE B 427 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 432 " --> pdb=" O ASP B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 455 removed outlier: 3.850A pdb=" N TYR B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET B 448 " --> pdb=" O TYR B 444 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 455 " --> pdb=" O GLY B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 466 removed outlier: 3.559A pdb=" N LYS B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 511 through 518 Processing helix chain 'B' and resid 531 through 540 removed outlier: 3.626A pdb=" N THR B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 557 removed outlier: 3.733A pdb=" N VAL B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 590 Processing helix chain 'B' and resid 615 through 623 removed outlier: 3.760A pdb=" N ARG B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 636 Processing helix chain 'B' and resid 648 through 661 removed outlier: 3.653A pdb=" N ASN B 655 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 681 removed outlier: 3.553A pdb=" N ASP B 670 " --> pdb=" O GLN B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 688 removed outlier: 4.204A pdb=" N ALA B 688 " --> pdb=" O ASP B 685 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 685 through 688' Processing helix chain 'B' and resid 689 through 701 removed outlier: 3.835A pdb=" N LEU B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 89 removed outlier: 3.519A pdb=" N ALA B 242 " --> pdb=" O GLN B 230 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG B 214 " --> pdb=" O HIS B 256 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 250 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 7.238A pdb=" N GLN A 91 " --> pdb=" O ILE B 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 291 removed outlier: 4.155A pdb=" N ARG A 214 " --> pdb=" O HIS A 256 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 233 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 245 Processing sheet with id=AA7, first strand: chain 'A' and resid 327 through 329 removed outlier: 3.915A pdb=" N TYR A 327 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 327 through 329 removed outlier: 3.915A pdb=" N TYR A 327 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 471 through 472 removed outlier: 3.874A pdb=" N GLU A 471 " --> pdb=" O PHE A 526 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 596 through 599 removed outlier: 6.606A pdb=" N ASN A 596 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ILE A 644 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LYS A 598 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 327 through 333 removed outlier: 3.750A pdb=" N TYR B 327 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 471 through 472 removed outlier: 9.285A pdb=" N LEU B 525 " --> pdb=" O ASN B 496 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR B 498 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N CYS B 527 " --> pdb=" O TYR B 498 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 500 " --> pdb=" O CYS B 527 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE B 497 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 597 through 599 removed outlier: 3.604A pdb=" N MET B 609 " --> pdb=" O GLU B 643 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1284 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: 3.54 Time building geometry restraints manager: 2.81 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: 3260 1.34 - 1.46: 2185 1.46 - 1.58: 4512 1.58 - 1.70: 6 1.70 - 1.82: 80 Bond restraints: 10043 Sorted by residual: bond pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.15e+01 bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" O5' ANP A 901 " pdb=" PA ANP A 901 " ideal model delta sigma weight residual 1.655 1.579 0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 10038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 13476 3.33 - 6.66: 64 6.66 - 10.00: 9 10.00 - 13.33: 2 13.33 - 16.66: 2 Bond angle restraints: 13553 Sorted by residual: angle pdb=" PB ANP A 901 " pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 126.95 110.29 16.66 3.00e+00 1.11e-01 3.08e+01 angle pdb=" PB ANP B 901 " pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 126.95 111.18 15.77 3.00e+00 1.11e-01 2.76e+01 angle pdb=" O1B ANP B 901 " pdb=" PB ANP B 901 " pdb=" O2B ANP B 901 " ideal model delta sigma weight residual 120.08 109.03 11.05 3.00e+00 1.11e-01 1.36e+01 angle pdb=" O1B ANP A 901 " pdb=" PB ANP A 901 " pdb=" O2B ANP A 901 " ideal model delta sigma weight residual 120.08 109.20 10.88 3.00e+00 1.11e-01 1.32e+01 angle pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " pdb=" O2G ANP A 901 " ideal model delta sigma weight residual 101.05 109.65 -8.60 3.00e+00 1.11e-01 8.22e+00 ... (remaining 13548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5491 17.90 - 35.80: 554 35.80 - 53.70: 93 53.70 - 71.59: 30 71.59 - 89.49: 13 Dihedral angle restraints: 6181 sinusoidal: 2583 harmonic: 3598 Sorted by residual: dihedral pdb=" CA LEU A 539 " pdb=" C LEU A 539 " pdb=" N ARG A 540 " pdb=" CA ARG A 540 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CG ARG A 658 " pdb=" CD ARG A 658 " pdb=" NE ARG A 658 " pdb=" CZ ARG A 658 " ideal model delta sinusoidal sigma weight residual 90.00 134.96 -44.96 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CA GLU B 633 " pdb=" C GLU B 633 " pdb=" N ARG B 634 " pdb=" CA ARG B 634 " ideal model delta harmonic sigma weight residual 180.00 163.78 16.22 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 6178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1280 0.056 - 0.111: 228 0.111 - 0.167: 18 0.167 - 0.223: 0 0.223 - 0.279: 2 Chirality restraints: 1528 Sorted by residual: chirality pdb=" C3' ANP B 901 " pdb=" C2' ANP B 901 " pdb=" C4' ANP B 901 " pdb=" O3' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C3' ANP A 901 " pdb=" C2' ANP A 901 " pdb=" C4' ANP A 901 " pdb=" O3' ANP A 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA ILE A 254 " pdb=" N ILE A 254 " pdb=" C ILE A 254 " pdb=" CB ILE A 254 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 1525 not shown) Planarity restraints: 1720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 639 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO B 640 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 640 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 640 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 585 " -0.010 2.00e-02 2.50e+03 1.05e-02 2.78e+00 pdb=" CG TRP B 585 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP B 585 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 585 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 585 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 585 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 585 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 585 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 585 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 585 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 621 " 0.008 2.00e-02 2.50e+03 9.18e-03 1.47e+00 pdb=" CG PHE A 621 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE A 621 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 621 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 621 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 621 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 621 " 0.001 2.00e-02 2.50e+03 ... (remaining 1717 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.61: 89 2.61 - 3.24: 9381 3.24 - 3.87: 18222 3.87 - 4.51: 24518 4.51 - 5.14: 40183 Nonbonded interactions: 92393 Sorted by model distance: nonbonded pdb=" OD1 ASN B 119 " pdb="MG MG B 902 " model vdw 1.974 2.170 nonbonded pdb=" O3G ANP B 901 " pdb="MG MG B 902 " model vdw 2.000 2.170 nonbonded pdb=" OD1 ASN A 119 " pdb="MG MG A 902 " model vdw 2.025 2.170 nonbonded pdb=" O3G ANP A 901 " pdb="MG MG A 902 " model vdw 2.038 2.170 nonbonded pdb=" O1B ANP A 901 " pdb="MG MG A 902 " model vdw 2.050 2.170 ... (remaining 92388 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 70 through 355 or resid 361 through 626 or resid 631 throu \ gh 704 or resid 901 through 903)) selection = (chain 'B' and (resid 70 through 355 or resid 361 through 625 or resid 631 or re \ sid 636 through 704 or resid 901 through 903)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 48.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.690 Find NCS groups from input model: 0.440 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 : 0.004 0.143 10044 Z= 0.190 Angle : 0.654 16.661 13553 Z= 0.320 Chirality : 0.042 0.279 1528 Planarity : 0.003 0.054 1720 Dihedral : 15.235 89.492 3843 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.09 % Allowed : 0.37 % Favored : 99.53 % 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: -0.12 (0.25), residues: 1210 helix: 1.04 (0.24), residues: 510 sheet: 0.36 (0.39), residues: 189 loop : -1.42 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 585 HIS 0.004 0.001 HIS A 88 PHE 0.021 0.001 PHE A 621 TYR 0.008 0.001 TYR B 206 ARG 0.012 0.001 ARG B 540 Details of bonding type rmsd hydrogen bonds : bond 0.19859 ( 459) hydrogen bonds : angle 6.48020 ( 1284) covalent geometry : bond 0.00383 (10043) covalent geometry : angle 0.65438 (13553) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 1.103 Fit side-chains REVERT: A 181 LYS cc_start: 0.8593 (mmmt) cc_final: 0.7953 (mtpp) REVERT: A 210 MET cc_start: 0.8400 (ttp) cc_final: 0.8127 (ptm) REVERT: A 309 TRP cc_start: 0.7420 (t-100) cc_final: 0.7109 (t-100) REVERT: A 490 MET cc_start: 0.8229 (ptp) cc_final: 0.7940 (ptp) REVERT: A 624 MET cc_start: 0.0541 (mtt) cc_final: 0.0311 (tpp) REVERT: A 689 MET cc_start: 0.8639 (ppp) cc_final: 0.7765 (ppp) REVERT: B 93 GLU cc_start: 0.8126 (tp30) cc_final: 0.7861 (tt0) REVERT: B 333 THR cc_start: 0.7945 (m) cc_final: 0.7616 (p) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.2404 time to fit residues: 42.1547 Evaluate side-chains 88 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 279 ASN A 288 ASN B 279 ASN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.115116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.086037 restraints weight = 17415.427| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.75 r_work: 0.2978 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10044 Z= 0.149 Angle : 0.566 8.939 13553 Z= 0.296 Chirality : 0.043 0.175 1528 Planarity : 0.004 0.032 1720 Dihedral : 6.659 57.906 1402 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.21 % Allowed : 7.38 % Favored : 91.41 % 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 (0.25), residues: 1210 helix: 1.26 (0.24), residues: 518 sheet: 0.38 (0.38), residues: 193 loop : -1.33 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 585 HIS 0.004 0.001 HIS A 88 PHE 0.012 0.001 PHE B 239 TYR 0.011 0.001 TYR B 437 ARG 0.004 0.000 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.04974 ( 459) hydrogen bonds : angle 4.73288 ( 1284) covalent geometry : bond 0.00355 (10043) covalent geometry : angle 0.56631 (13553) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.096 Fit side-chains REVERT: A 181 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8050 (mtpp) REVERT: A 309 TRP cc_start: 0.7654 (t-100) cc_final: 0.7328 (t-100) REVERT: B 93 GLU cc_start: 0.8551 (tp30) cc_final: 0.8272 (tp30) REVERT: B 333 THR cc_start: 0.8307 (m) cc_final: 0.8079 (p) outliers start: 13 outliers final: 9 residues processed: 105 average time/residue: 0.2471 time to fit residues: 36.7991 Evaluate side-chains 94 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 657 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 111 optimal weight: 0.4980 chunk 104 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS A 666 GLN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.116309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.087055 restraints weight = 17595.446| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.80 r_work: 0.2991 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10044 Z= 0.108 Angle : 0.510 8.974 13553 Z= 0.266 Chirality : 0.041 0.156 1528 Planarity : 0.003 0.028 1720 Dihedral : 6.085 59.633 1402 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.68 % Allowed : 9.43 % Favored : 88.89 % 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: 0.36 (0.25), residues: 1210 helix: 1.53 (0.24), residues: 515 sheet: 0.41 (0.38), residues: 194 loop : -1.22 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 585 HIS 0.005 0.001 HIS A 88 PHE 0.010 0.001 PHE B 239 TYR 0.010 0.001 TYR B 206 ARG 0.003 0.000 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 459) hydrogen bonds : angle 4.28950 ( 1284) covalent geometry : bond 0.00250 (10043) covalent geometry : angle 0.50962 (13553) Misc. bond : bond 0.00092 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 1.536 Fit side-chains REVERT: A 181 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8064 (mtpp) REVERT: A 309 TRP cc_start: 0.7691 (t-100) cc_final: 0.7400 (t-100) REVERT: A 624 MET cc_start: 0.1335 (mtt) cc_final: 0.0779 (ttt) REVERT: B 93 GLU cc_start: 0.8569 (tp30) cc_final: 0.8291 (tp30) REVERT: B 333 THR cc_start: 0.8336 (m) cc_final: 0.8037 (p) REVERT: B 656 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.7005 (mp10) REVERT: B 666 GLN cc_start: 0.8591 (tp-100) cc_final: 0.8340 (tp40) outliers start: 18 outliers final: 13 residues processed: 105 average time/residue: 0.3645 time to fit residues: 54.8660 Evaluate side-chains 104 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 657 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 117 optimal weight: 0.0970 chunk 81 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.112743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.083334 restraints weight = 17452.592| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.79 r_work: 0.2921 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10044 Z= 0.211 Angle : 0.598 8.603 13553 Z= 0.312 Chirality : 0.045 0.158 1528 Planarity : 0.004 0.031 1720 Dihedral : 6.819 59.889 1402 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.33 % Allowed : 11.39 % Favored : 86.27 % 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: 0.02 (0.25), residues: 1210 helix: 1.35 (0.24), residues: 522 sheet: 0.12 (0.38), residues: 195 loop : -1.53 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 585 HIS 0.005 0.001 HIS B 620 PHE 0.014 0.002 PHE A 531 TYR 0.017 0.002 TYR B 437 ARG 0.004 0.000 ARG A 402 Details of bonding type rmsd hydrogen bonds : bond 0.05121 ( 459) hydrogen bonds : angle 4.39592 ( 1284) covalent geometry : bond 0.00519 (10043) covalent geometry : angle 0.59810 (13553) Misc. bond : bond 0.00175 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 181 LYS cc_start: 0.8679 (mmmt) cc_final: 0.8076 (mtpp) REVERT: A 309 TRP cc_start: 0.7764 (t-100) cc_final: 0.7476 (t-100) REVERT: B 93 GLU cc_start: 0.8641 (tp30) cc_final: 0.8350 (tp30) outliers start: 25 outliers final: 17 residues processed: 104 average time/residue: 0.2953 time to fit residues: 43.6202 Evaluate side-chains 104 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 657 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 104 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 479 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 = 0.3571 r_free = 0.3571 target = 0.114522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.085252 restraints weight = 17423.958| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.77 r_work: 0.2959 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10044 Z= 0.132 Angle : 0.519 7.822 13553 Z= 0.272 Chirality : 0.042 0.149 1528 Planarity : 0.003 0.029 1720 Dihedral : 6.161 57.038 1402 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.43 % Allowed : 12.04 % Favored : 85.53 % 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 (0.25), residues: 1210 helix: 1.54 (0.24), residues: 522 sheet: 0.16 (0.38), residues: 194 loop : -1.39 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 585 HIS 0.004 0.001 HIS A 88 PHE 0.012 0.001 PHE B 239 TYR 0.011 0.001 TYR B 206 ARG 0.003 0.000 ARG B 658 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 459) hydrogen bonds : angle 4.19748 ( 1284) covalent geometry : bond 0.00316 (10043) covalent geometry : angle 0.51879 (13553) Misc. bond : bond 0.00124 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 1.197 Fit side-chains REVERT: A 181 LYS cc_start: 0.8681 (mmmt) cc_final: 0.8072 (mtpp) REVERT: A 309 TRP cc_start: 0.7732 (t-100) cc_final: 0.7471 (t-100) REVERT: A 352 MET cc_start: 0.3176 (OUTLIER) cc_final: 0.2714 (tpp) REVERT: B 93 GLU cc_start: 0.8570 (tp30) cc_final: 0.8289 (tp30) REVERT: B 352 MET cc_start: 0.5624 (mmm) cc_final: 0.5271 (ttm) REVERT: B 636 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7684 (mt0) outliers start: 26 outliers final: 15 residues processed: 106 average time/residue: 0.2355 time to fit residues: 35.7432 Evaluate side-chains 109 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 657 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 0.0060 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 77 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 HIS ** B 479 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 = 0.3598 r_free = 0.3598 target = 0.116448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.087094 restraints weight = 17458.911| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.80 r_work: 0.2990 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10044 Z= 0.095 Angle : 0.486 7.786 13553 Z= 0.254 Chirality : 0.040 0.144 1528 Planarity : 0.003 0.027 1720 Dihedral : 5.505 53.613 1402 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.96 % Allowed : 12.61 % Favored : 85.43 % 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: 0.43 (0.25), residues: 1210 helix: 1.72 (0.24), residues: 522 sheet: 0.29 (0.39), residues: 196 loop : -1.32 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 585 HIS 0.005 0.001 HIS A 88 PHE 0.012 0.001 PHE B 621 TYR 0.009 0.001 TYR B 206 ARG 0.007 0.000 ARG B 495 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 459) hydrogen bonds : angle 4.03701 ( 1284) covalent geometry : bond 0.00217 (10043) covalent geometry : angle 0.48604 (13553) Misc. bond : bond 0.00072 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 1.240 Fit side-chains REVERT: A 181 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8044 (mtpp) REVERT: A 309 TRP cc_start: 0.7734 (t-100) cc_final: 0.7517 (t-100) REVERT: A 352 MET cc_start: 0.3392 (OUTLIER) cc_final: 0.3019 (tpp) REVERT: B 93 GLU cc_start: 0.8545 (tp30) cc_final: 0.8291 (tp30) REVERT: B 352 MET cc_start: 0.5548 (mmm) cc_final: 0.5235 (ttm) REVERT: B 636 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7648 (mt0) outliers start: 21 outliers final: 16 residues processed: 106 average time/residue: 0.2609 time to fit residues: 38.6683 Evaluate side-chains 107 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 657 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 479 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 = 0.3547 r_free = 0.3547 target = 0.112922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.083519 restraints weight = 17704.905| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.79 r_work: 0.2924 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10044 Z= 0.200 Angle : 0.587 7.801 13553 Z= 0.306 Chirality : 0.044 0.157 1528 Planarity : 0.004 0.046 1720 Dihedral : 6.520 57.776 1402 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.71 % Allowed : 13.07 % Favored : 84.22 % 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: 0.20 (0.25), residues: 1210 helix: 1.58 (0.24), residues: 523 sheet: 0.13 (0.38), residues: 196 loop : -1.50 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 585 HIS 0.004 0.001 HIS B 330 PHE 0.012 0.002 PHE B 239 TYR 0.016 0.002 TYR B 437 ARG 0.004 0.000 ARG B 495 Details of bonding type rmsd hydrogen bonds : bond 0.04800 ( 459) hydrogen bonds : angle 4.20298 ( 1284) covalent geometry : bond 0.00490 (10043) covalent geometry : angle 0.58658 (13553) Misc. bond : bond 0.00161 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 1.120 Fit side-chains REVERT: A 181 LYS cc_start: 0.8670 (mmmt) cc_final: 0.8084 (mtpp) REVERT: A 309 TRP cc_start: 0.7762 (t-100) cc_final: 0.7537 (t-100) REVERT: A 352 MET cc_start: 0.3071 (OUTLIER) cc_final: 0.2591 (tpp) REVERT: A 583 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7000 (mpp) REVERT: A 624 MET cc_start: 0.1163 (OUTLIER) cc_final: 0.0923 (tpp) REVERT: B 352 MET cc_start: 0.5441 (mmm) cc_final: 0.5159 (ttm) REVERT: B 546 LYS cc_start: 0.8193 (mppt) cc_final: 0.7742 (mptt) REVERT: B 636 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7763 (mt0) outliers start: 29 outliers final: 22 residues processed: 106 average time/residue: 0.2430 time to fit residues: 36.3381 Evaluate side-chains 110 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 660 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 26 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.116008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.086559 restraints weight = 17545.796| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.81 r_work: 0.2979 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10044 Z= 0.102 Angle : 0.509 7.537 13553 Z= 0.265 Chirality : 0.041 0.149 1528 Planarity : 0.003 0.034 1720 Dihedral : 5.570 51.786 1402 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.24 % Allowed : 13.82 % Favored : 83.94 % 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: 0.47 (0.25), residues: 1210 helix: 1.81 (0.24), residues: 519 sheet: 0.28 (0.39), residues: 194 loop : -1.35 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 585 HIS 0.005 0.001 HIS A 88 PHE 0.023 0.001 PHE B 621 TYR 0.009 0.001 TYR B 206 ARG 0.006 0.000 ARG B 495 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 459) hydrogen bonds : angle 4.01064 ( 1284) covalent geometry : bond 0.00236 (10043) covalent geometry : angle 0.50866 (13553) Misc. bond : bond 0.00082 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.214 Fit side-chains REVERT: A 181 LYS cc_start: 0.8660 (mmmt) cc_final: 0.8057 (mtpp) REVERT: A 352 MET cc_start: 0.3058 (OUTLIER) cc_final: 0.2693 (tpp) REVERT: A 583 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7069 (mpp) REVERT: A 624 MET cc_start: 0.1165 (OUTLIER) cc_final: 0.0934 (tpp) REVERT: B 93 GLU cc_start: 0.8582 (tp30) cc_final: 0.8347 (tp30) REVERT: B 309 TRP cc_start: 0.7769 (t60) cc_final: 0.7523 (t60) REVERT: B 352 MET cc_start: 0.5401 (mmm) cc_final: 0.5171 (ttm) REVERT: B 546 LYS cc_start: 0.8127 (mppt) cc_final: 0.7693 (mptt) REVERT: B 636 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7725 (mt0) outliers start: 24 outliers final: 17 residues processed: 105 average time/residue: 0.2530 time to fit residues: 37.0919 Evaluate side-chains 109 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 660 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 26 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 479 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 = 0.3579 r_free = 0.3579 target = 0.115286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.085827 restraints weight = 17558.501| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.80 r_work: 0.2969 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10044 Z= 0.123 Angle : 0.524 7.711 13553 Z= 0.273 Chirality : 0.041 0.152 1528 Planarity : 0.003 0.051 1720 Dihedral : 5.811 56.516 1402 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.43 % Allowed : 13.82 % Favored : 83.75 % 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: 0.42 (0.25), residues: 1210 helix: 1.75 (0.24), residues: 527 sheet: 0.30 (0.39), residues: 194 loop : -1.41 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 585 HIS 0.004 0.001 HIS A 88 PHE 0.011 0.001 PHE A 531 TYR 0.011 0.001 TYR B 206 ARG 0.007 0.000 ARG B 495 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 459) hydrogen bonds : angle 4.00787 ( 1284) covalent geometry : bond 0.00293 (10043) covalent geometry : angle 0.52403 (13553) Misc. bond : bond 0.00103 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 1.049 Fit side-chains REVERT: A 181 LYS cc_start: 0.8649 (mmmt) cc_final: 0.8055 (mtpp) REVERT: A 583 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7118 (mpp) REVERT: A 624 MET cc_start: 0.1135 (OUTLIER) cc_final: 0.0906 (tpp) REVERT: B 352 MET cc_start: 0.5405 (mmm) cc_final: 0.5182 (ttm) REVERT: B 546 LYS cc_start: 0.8147 (mppt) cc_final: 0.7734 (mptt) REVERT: B 636 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7713 (mt0) outliers start: 26 outliers final: 21 residues processed: 100 average time/residue: 0.2599 time to fit residues: 36.6366 Evaluate side-chains 111 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 660 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 60 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 65 optimal weight: 0.0040 chunk 18 optimal weight: 4.9990 chunk 87 optimal weight: 0.3980 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 479 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.117197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.087712 restraints weight = 17520.387| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.83 r_work: 0.3005 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10044 Z= 0.090 Angle : 0.486 7.799 13553 Z= 0.253 Chirality : 0.040 0.145 1528 Planarity : 0.003 0.057 1720 Dihedral : 5.249 47.805 1402 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.15 % Allowed : 14.01 % Favored : 83.85 % 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: 0.63 (0.25), residues: 1210 helix: 1.92 (0.24), residues: 519 sheet: 0.36 (0.39), residues: 194 loop : -1.22 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 231 HIS 0.005 0.001 HIS A 88 PHE 0.024 0.001 PHE B 621 TYR 0.008 0.001 TYR B 206 ARG 0.008 0.000 ARG B 495 Details of bonding type rmsd hydrogen bonds : bond 0.03066 ( 459) hydrogen bonds : angle 3.90471 ( 1284) covalent geometry : bond 0.00203 (10043) covalent geometry : angle 0.48572 (13553) Misc. bond : bond 0.00072 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 2.032 Fit side-chains REVERT: A 181 LYS cc_start: 0.8646 (mmmt) cc_final: 0.8062 (mtpp) REVERT: A 583 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7200 (mpp) REVERT: A 624 MET cc_start: 0.1088 (OUTLIER) cc_final: 0.0851 (tpp) REVERT: B 93 GLU cc_start: 0.8502 (tp30) cc_final: 0.8277 (tp30) REVERT: B 309 TRP cc_start: 0.7757 (t60) cc_final: 0.7541 (t60) REVERT: B 546 LYS cc_start: 0.8130 (mppt) cc_final: 0.7730 (mptt) REVERT: B 636 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7686 (mt0) outliers start: 23 outliers final: 19 residues processed: 105 average time/residue: 0.3518 time to fit residues: 52.7530 Evaluate side-chains 110 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 657 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 106 optimal weight: 0.0270 chunk 19 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.115856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.086565 restraints weight = 17504.674| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.80 r_work: 0.2979 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10044 Z= 0.108 Angle : 0.517 9.803 13553 Z= 0.267 Chirality : 0.040 0.149 1528 Planarity : 0.003 0.064 1720 Dihedral : 5.515 53.586 1402 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.33 % Allowed : 14.01 % Favored : 83.66 % 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: 0.70 (0.25), residues: 1210 helix: 2.04 (0.24), residues: 511 sheet: 0.34 (0.39), residues: 194 loop : -1.19 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 231 HIS 0.004 0.001 HIS A 88 PHE 0.009 0.001 PHE B 239 TYR 0.010 0.001 TYR B 206 ARG 0.009 0.000 ARG B 495 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 459) hydrogen bonds : angle 3.91550 ( 1284) covalent geometry : bond 0.00255 (10043) covalent geometry : angle 0.51679 (13553) Misc. bond : bond 0.00083 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5504.01 seconds wall clock time: 101 minutes 4.08 seconds (6064.08 seconds total)