Starting phenix.real_space_refine on Wed Mar 4 03:26:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7klv_22919/03_2026/7klv_22919.cif Found real_map, /net/cci-nas-00/data/ceres_data/7klv_22919/03_2026/7klv_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 { model { file = "/net/cci-nas-00/data/ceres_data/7klv_22919/03_2026/7klv_22919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7klv_22919/03_2026/7klv_22919.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7klv_22919/03_2026/7klv_22919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7klv_22919/03_2026/7klv_22919.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.38, per 1000 atoms: 0.24 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: 0.82 Conformation dependent library (CDL) restraints added in 434.4 milliseconds 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: 0.31 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: 1.36 Time building geometry restraints manager: 1.10 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 903)) selection = (chain 'B' and (resid 70 through 355 or resid 361 through 625 or resid 631 or re \ sid 636 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: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.440 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.980 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (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 ARG 0.012 0.001 ARG B 540 TYR 0.008 0.001 TYR B 206 PHE 0.021 0.001 PHE A 621 TRP 0.029 0.002 TRP B 585 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00383 (10043) covalent geometry : angle 0.65438 (13553) hydrogen bonds : bond 0.19859 ( 459) hydrogen bonds : angle 6.48020 ( 1284) 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 : 0.294 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: 0.1128 time to fit residues: 19.8075 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 : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 190 GLN ** B 479 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 = 0.3543 r_free = 0.3543 target = 0.112481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.083107 restraints weight = 17669.058| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.80 r_work: 0.2921 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10044 Z= 0.249 Angle : 0.654 9.592 13553 Z= 0.342 Chirality : 0.047 0.180 1528 Planarity : 0.004 0.035 1720 Dihedral : 7.169 59.397 1402 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.31 % Allowed : 8.68 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.25), residues: 1210 helix: 1.05 (0.24), residues: 525 sheet: 0.19 (0.38), residues: 195 loop : -1.57 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 402 TYR 0.016 0.002 TYR B 437 PHE 0.017 0.002 PHE B 239 TRP 0.018 0.002 TRP B 585 HIS 0.005 0.001 HIS A 538 Details of bonding type rmsd covalent geometry : bond 0.00608 (10043) covalent geometry : angle 0.65399 (13553) hydrogen bonds : bond 0.05893 ( 459) hydrogen bonds : angle 4.91605 ( 1284) Misc. bond : bond 0.00167 ( 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 108 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.353 Fit side-chains REVERT: A 181 LYS cc_start: 0.8685 (mmmt) cc_final: 0.8096 (mtpp) REVERT: A 309 TRP cc_start: 0.7724 (t-100) cc_final: 0.7380 (t-100) REVERT: B 93 GLU cc_start: 0.8613 (tp30) cc_final: 0.8304 (tp30) REVERT: B 624 MET cc_start: 0.5096 (mtt) cc_final: 0.4844 (mtp) outliers start: 14 outliers final: 10 residues processed: 102 average time/residue: 0.1143 time to fit residues: 16.0300 Evaluate side-chains 92 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 337 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 67 optimal weight: 0.0030 chunk 51 optimal weight: 0.0770 chunk 4 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 40 optimal weight: 0.0470 chunk 18 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 overall best weight: 0.3246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS B 190 GLN B 279 ASN B 311 HIS ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.118068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.088980 restraints weight = 17503.812| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.81 r_work: 0.3028 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1525 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= 0.087 Angle : 0.487 7.683 13553 Z= 0.255 Chirality : 0.041 0.149 1528 Planarity : 0.003 0.028 1720 Dihedral : 5.766 56.187 1402 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.21 % Allowed : 11.30 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.25), residues: 1210 helix: 1.54 (0.24), residues: 514 sheet: 0.38 (0.39), residues: 194 loop : -1.25 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 587 TYR 0.009 0.001 TYR B 206 PHE 0.008 0.001 PHE B 531 TRP 0.012 0.002 TRP A 231 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00182 (10043) covalent geometry : angle 0.48706 (13553) hydrogen bonds : bond 0.03353 ( 459) hydrogen bonds : angle 4.32429 ( 1284) Misc. bond : bond 0.00060 ( 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: 13 poor density : 102 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 181 LYS cc_start: 0.8636 (mmmt) cc_final: 0.8070 (mtpp) REVERT: A 309 TRP cc_start: 0.7633 (t-100) cc_final: 0.7394 (t-100) REVERT: B 93 GLU cc_start: 0.8525 (tp30) cc_final: 0.8260 (tp30) REVERT: B 333 THR cc_start: 0.8312 (m) cc_final: 0.8033 (p) REVERT: B 656 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.7003 (mp10) REVERT: B 666 GLN cc_start: 0.8552 (tp-100) cc_final: 0.8300 (tp40) outliers start: 13 outliers final: 9 residues processed: 109 average time/residue: 0.1022 time to fit residues: 15.3897 Evaluate side-chains 101 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 379 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 656 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 23 optimal weight: 0.0370 chunk 115 optimal weight: 0.0020 chunk 15 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.5468 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.117704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.088418 restraints weight = 17582.872| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.81 r_work: 0.3016 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1670 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= 0.087 Angle : 0.473 7.604 13553 Z= 0.247 Chirality : 0.040 0.148 1528 Planarity : 0.003 0.027 1720 Dihedral : 5.454 50.435 1402 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.87 % Allowed : 11.95 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.25), residues: 1210 helix: 1.77 (0.24), residues: 514 sheet: 0.44 (0.39), residues: 196 loop : -1.14 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 128 TYR 0.009 0.001 TYR B 206 PHE 0.014 0.001 PHE A 531 TRP 0.011 0.002 TRP B 309 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00191 (10043) covalent geometry : angle 0.47257 (13553) hydrogen bonds : bond 0.03259 ( 459) hydrogen bonds : angle 4.10810 ( 1284) Misc. bond : bond 0.00061 ( 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 117 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8034 (mtpp) REVERT: A 309 TRP cc_start: 0.7659 (t-100) cc_final: 0.7423 (t-100) REVERT: A 485 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7972 (mp0) REVERT: A 586 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.6978 (mpp) REVERT: B 93 GLU cc_start: 0.8530 (tp30) cc_final: 0.8266 (tp30) REVERT: B 333 THR cc_start: 0.8347 (m) cc_final: 0.8097 (p) REVERT: B 656 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: B 666 GLN cc_start: 0.8492 (tp-100) cc_final: 0.8292 (tp40) outliers start: 20 outliers final: 13 residues processed: 111 average time/residue: 0.1042 time to fit residues: 16.3342 Evaluate side-chains 106 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 446 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 636 GLN Chi-restraints excluded: chain B residue 656 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 16 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.114276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.084882 restraints weight = 17685.365| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.83 r_work: 0.2952 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10044 Z= 0.154 Angle : 0.536 7.269 13553 Z= 0.280 Chirality : 0.042 0.151 1528 Planarity : 0.003 0.031 1720 Dihedral : 6.152 59.409 1402 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.71 % Allowed : 11.58 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.25), residues: 1210 helix: 1.68 (0.24), residues: 522 sheet: 0.29 (0.39), residues: 195 loop : -1.30 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 658 TYR 0.013 0.001 TYR B 437 PHE 0.011 0.001 PHE B 239 TRP 0.012 0.002 TRP B 309 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00373 (10043) covalent geometry : angle 0.53607 (13553) hydrogen bonds : bond 0.04287 ( 459) hydrogen bonds : angle 4.20080 ( 1284) Misc. bond : bond 0.00126 ( 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 124 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 181 LYS cc_start: 0.8688 (mmmt) cc_final: 0.8092 (mtpp) REVERT: A 309 TRP cc_start: 0.7747 (t-100) cc_final: 0.7495 (t-100) REVERT: A 583 MET cc_start: 0.7964 (mpp) cc_final: 0.7098 (mpp) REVERT: B 93 GLU cc_start: 0.8567 (tp30) cc_final: 0.8294 (tp30) outliers start: 29 outliers final: 19 residues processed: 112 average time/residue: 0.0958 time to fit residues: 15.0085 Evaluate side-chains 107 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 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 194 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 328 THR 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 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 106 optimal weight: 5.9990 chunk 16 optimal weight: 0.0770 chunk 84 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.9540 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.115987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.086554 restraints weight = 17647.379| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.82 r_work: 0.2983 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10044 Z= 0.103 Angle : 0.487 6.780 13553 Z= 0.255 Chirality : 0.041 0.145 1528 Planarity : 0.003 0.028 1720 Dihedral : 5.551 53.563 1402 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.68 % Allowed : 12.23 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.25), residues: 1210 helix: 1.78 (0.24), residues: 522 sheet: 0.36 (0.39), residues: 195 loop : -1.27 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 658 TYR 0.010 0.001 TYR B 206 PHE 0.009 0.001 PHE B 239 TRP 0.010 0.002 TRP A 231 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00239 (10043) covalent geometry : angle 0.48689 (13553) hydrogen bonds : bond 0.03530 ( 459) hydrogen bonds : angle 4.05692 ( 1284) Misc. bond : bond 0.00094 ( 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 112 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 181 LYS cc_start: 0.8636 (mmmt) cc_final: 0.8050 (mtpp) REVERT: A 309 TRP cc_start: 0.7718 (t-100) cc_final: 0.7487 (t-100) REVERT: A 485 GLU cc_start: 0.8495 (mp0) cc_final: 0.8138 (mp0) REVERT: A 583 MET cc_start: 0.7944 (mpp) cc_final: 0.7145 (mpp) REVERT: B 93 GLU cc_start: 0.8537 (tp30) cc_final: 0.8285 (tp30) outliers start: 18 outliers final: 16 residues processed: 104 average time/residue: 0.1069 time to fit residues: 15.4232 Evaluate side-chains 107 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 379 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 501 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 396 ILE 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 121 optimal weight: 0.0670 chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 GLN ** 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 = 0.3610 r_free = 0.3610 target = 0.117149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.087808 restraints weight = 17606.934| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.82 r_work: 0.3003 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1972 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= 0.089 Angle : 0.479 7.555 13553 Z= 0.250 Chirality : 0.040 0.145 1528 Planarity : 0.003 0.026 1720 Dihedral : 5.279 48.972 1402 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.96 % Allowed : 12.79 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.25), residues: 1210 helix: 1.90 (0.24), residues: 519 sheet: 0.45 (0.40), residues: 195 loop : -1.24 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 495 TYR 0.009 0.001 TYR B 206 PHE 0.015 0.001 PHE B 621 TRP 0.016 0.002 TRP B 309 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00200 (10043) covalent geometry : angle 0.47919 (13553) hydrogen bonds : bond 0.03176 ( 459) hydrogen bonds : angle 3.96974 ( 1284) Misc. bond : bond 0.00070 ( 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 117 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 181 LYS cc_start: 0.8627 (mmmt) cc_final: 0.8036 (mtpp) REVERT: A 583 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7173 (mpp) REVERT: A 585 TRP cc_start: 0.7980 (t60) cc_final: 0.7706 (t60) REVERT: A 655 ASN cc_start: 0.7460 (t0) cc_final: 0.7075 (p0) REVERT: B 93 GLU cc_start: 0.8510 (tp30) cc_final: 0.8270 (tp30) REVERT: B 333 THR cc_start: 0.8437 (m) cc_final: 0.8084 (p) outliers start: 21 outliers final: 15 residues processed: 107 average time/residue: 0.1007 time to fit residues: 15.2682 Evaluate side-chains 107 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 379 ILE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 446 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 117 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 GLN ** 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 = 0.3585 r_free = 0.3585 target = 0.115406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.085917 restraints weight = 17530.667| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.81 r_work: 0.2972 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10044 Z= 0.123 Angle : 0.522 9.337 13553 Z= 0.269 Chirality : 0.041 0.147 1528 Planarity : 0.003 0.029 1720 Dihedral : 5.771 57.274 1402 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.24 % Allowed : 12.70 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.25), residues: 1210 helix: 1.90 (0.24), residues: 519 sheet: 0.35 (0.39), residues: 195 loop : -1.28 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 495 TYR 0.011 0.001 TYR B 437 PHE 0.010 0.001 PHE A 531 TRP 0.018 0.002 TRP B 309 HIS 0.003 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00295 (10043) covalent geometry : angle 0.52194 (13553) hydrogen bonds : bond 0.03780 ( 459) hydrogen bonds : angle 4.02557 ( 1284) Misc. bond : bond 0.00105 ( 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 115 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 181 LYS cc_start: 0.8680 (mmmt) cc_final: 0.8091 (mtpp) REVERT: A 583 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7137 (mpp) REVERT: B 93 GLU cc_start: 0.8567 (tp30) cc_final: 0.8321 (tp30) outliers start: 24 outliers final: 22 residues processed: 104 average time/residue: 0.0996 time to fit residues: 14.5059 Evaluate side-chains 112 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 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 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 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 636 GLN Chi-restraints excluded: chain B residue 657 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 32 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 0.0770 chunk 85 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 61 optimal weight: 0.0010 overall best weight: 0.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 GLN B 479 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.118459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.089120 restraints weight = 17522.374| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.82 r_work: 0.3029 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10044 Z= 0.083 Angle : 0.481 8.458 13553 Z= 0.247 Chirality : 0.040 0.148 1528 Planarity : 0.003 0.047 1720 Dihedral : 5.026 43.857 1402 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.77 % Allowed : 13.35 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.25), residues: 1210 helix: 1.96 (0.24), residues: 520 sheet: 0.44 (0.39), residues: 195 loop : -1.18 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 495 TYR 0.008 0.001 TYR B 206 PHE 0.006 0.001 PHE B 239 TRP 0.014 0.002 TRP B 309 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00182 (10043) covalent geometry : angle 0.48104 (13553) hydrogen bonds : bond 0.02843 ( 459) hydrogen bonds : angle 3.89769 ( 1284) Misc. bond : bond 0.00058 ( 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 117 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.284 Fit side-chains REVERT: A 181 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8040 (mtpp) REVERT: A 585 TRP cc_start: 0.7910 (t60) cc_final: 0.7643 (t60) REVERT: B 93 GLU cc_start: 0.8498 (tp30) cc_final: 0.8261 (tp30) REVERT: B 333 THR cc_start: 0.8448 (m) cc_final: 0.8112 (p) REVERT: B 352 MET cc_start: 0.5550 (mmm) cc_final: 0.5194 (ttm) REVERT: B 546 LYS cc_start: 0.8109 (mppt) cc_final: 0.7670 (mptt) REVERT: B 636 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7677 (mt0) outliers start: 19 outliers final: 14 residues processed: 108 average time/residue: 0.1026 time to fit residues: 15.4965 Evaluate side-chains 106 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 348 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 496 ASN 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 = 0.116265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.086728 restraints weight = 17288.849| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.81 r_work: 0.2981 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2134 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= 0.116 Angle : 0.525 8.560 13553 Z= 0.270 Chirality : 0.041 0.152 1528 Planarity : 0.004 0.072 1720 Dihedral : 5.619 55.878 1402 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.49 % Allowed : 14.10 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.25), residues: 1210 helix: 2.06 (0.24), residues: 513 sheet: 0.40 (0.39), residues: 195 loop : -1.23 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 495 TYR 0.011 0.001 TYR B 437 PHE 0.025 0.001 PHE B 621 TRP 0.019 0.002 TRP B 309 HIS 0.003 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00274 (10043) covalent geometry : angle 0.52542 (13553) hydrogen bonds : bond 0.03575 ( 459) hydrogen bonds : angle 3.97496 ( 1284) Misc. bond : bond 0.00097 ( 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 108 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 181 LYS cc_start: 0.8672 (mmmt) cc_final: 0.8086 (mtpp) REVERT: A 585 TRP cc_start: 0.7998 (t60) cc_final: 0.7733 (t60) REVERT: B 93 GLU cc_start: 0.8557 (tp30) cc_final: 0.8315 (tp30) REVERT: B 352 MET cc_start: 0.5564 (mmm) cc_final: 0.5195 (ttm) REVERT: B 546 LYS cc_start: 0.8141 (mppt) cc_final: 0.7718 (mptt) outliers start: 16 outliers final: 16 residues processed: 100 average time/residue: 0.1027 time to fit residues: 14.4888 Evaluate side-chains 105 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 39 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 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 496 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.117099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.087645 restraints weight = 17405.011| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.82 r_work: 0.3002 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10044 Z= 0.099 Angle : 0.511 8.385 13553 Z= 0.263 Chirality : 0.040 0.151 1528 Planarity : 0.003 0.063 1720 Dihedral : 5.394 51.875 1402 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.68 % Allowed : 13.91 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.25), residues: 1210 helix: 2.08 (0.24), residues: 513 sheet: 0.40 (0.39), residues: 195 loop : -1.22 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 495 TYR 0.009 0.001 TYR B 206 PHE 0.027 0.001 PHE A 531 TRP 0.018 0.002 TRP B 309 HIS 0.003 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00228 (10043) covalent geometry : angle 0.51062 (13553) hydrogen bonds : bond 0.03280 ( 459) hydrogen bonds : angle 3.94092 ( 1284) Misc. bond : bond 0.00082 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2193.71 seconds wall clock time: 38 minutes 18.12 seconds (2298.12 seconds total)