Starting phenix.real_space_refine on Sat Feb 17 17:16:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3x_27167/02_2024/8d3x_27167_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3x_27167/02_2024/8d3x_27167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3x_27167/02_2024/8d3x_27167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3x_27167/02_2024/8d3x_27167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3x_27167/02_2024/8d3x_27167_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3x_27167/02_2024/8d3x_27167_updated.pdb" } resolution = 4.1 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= 0.004 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 9217 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: 6 Type Number sf(0) Gaussians Mg 1 5.21 5 S 61 5.16 5 C 6531 2.51 5 N 1704 2.21 5 O 1918 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A GLU 889": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10219 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2322 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 264} Chain: "G" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 246 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "A" Number of atoms: 7651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7651 Unusual residues: {'MF4': 1} Inner-chain residues flagged as termini: ['pdbres="TYR A1013 "'] Classifications: {'peptide': 989, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 947, None: 1} Not linked: pdbres="TYR A1013 " pdbres="MF4 A2101 " Time building chain proxies: 6.03, per 1000 atoms: 0.59 Number of scatterers: 10219 At special positions: 0 Unit cell: (146.08, 106.24, 141.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 61 16.00 Mg 1 11.99 F 4 9.00 O 1918 8.00 N 1704 7.00 C 6531 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 239 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.48 Conformation dependent library (CDL) restraints added in 2.0 seconds 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 10 sheets defined 40.4% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'B' and resid 34 through 60 removed outlier: 3.532A pdb=" N THR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 112 removed outlier: 4.730A pdb=" N LYS B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TYR B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'G' and resid 37 through 57 removed outlier: 3.525A pdb=" N LEU G 55 " --> pdb=" O VAL G 51 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE G 56 " --> pdb=" O GLY G 52 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU G 57 " --> pdb=" O ILE G 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 55 through 65 removed outlier: 3.917A pdb=" N ARG A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 87 Processing helix chain 'A' and resid 92 through 108 Processing helix chain 'A' and resid 120 through 137 Processing helix chain 'A' and resid 147 through 150 removed outlier: 3.575A pdb=" N SER A 150 " --> pdb=" O ILE A 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 150' Processing helix chain 'A' and resid 256 through 267 Processing helix chain 'A' and resid 273 through 303 Processing helix chain 'A' and resid 307 through 321 Processing helix chain 'A' and resid 327 through 344 removed outlier: 3.870A pdb=" N THR A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS A 344 " --> pdb=" O ARG A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 removed outlier: 3.709A pdb=" N VAL A 354 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A 357 " --> pdb=" O VAL A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 417 Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 457 through 463 Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 522 through 538 removed outlier: 3.739A pdb=" N LEU A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 599 Processing helix chain 'A' and resid 611 through 621 Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 660 through 662 No H-bonds generated for 'chain 'A' and resid 660 through 662' Processing helix chain 'A' and resid 665 through 674 Processing helix chain 'A' and resid 685 through 698 removed outlier: 3.699A pdb=" N GLN A 698 " --> pdb=" O GLY A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 717 Proline residue: A 713 - end of helix Processing helix chain 'A' and resid 730 through 734 Processing helix chain 'A' and resid 745 through 785 removed outlier: 3.517A pdb=" N LYS A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA A 767 " --> pdb=" O LYS A 763 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN A 773 " --> pdb=" O THR A 769 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) Proline residue: A 775 - end of helix Proline residue: A 779 - end of helix Processing helix chain 'A' and resid 795 through 803 Processing helix chain 'A' and resid 807 through 813 removed outlier: 3.995A pdb=" N ALA A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 823 removed outlier: 4.128A pdb=" N MET A 822 " --> pdb=" O SER A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 844 removed outlier: 3.577A pdb=" N SER A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET A 842 " --> pdb=" O ARG A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 864 Processing helix chain 'A' and resid 877 through 880 No H-bonds generated for 'chain 'A' and resid 877 through 880' Processing helix chain 'A' and resid 898 through 927 removed outlier: 3.807A pdb=" N VAL A 904 " --> pdb=" O GLN A 900 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A 922 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 937 No H-bonds generated for 'chain 'A' and resid 934 through 937' Processing helix chain 'A' and resid 942 through 958 removed outlier: 3.932A pdb=" N PHE A 946 " --> pdb=" O LYS A 942 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 975 through 979 Processing helix chain 'A' and resid 982 through 1001 removed outlier: 4.501A pdb=" N LEU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1011 Processing sheet with id= A, first strand: chain 'B' and resid 87 through 90 removed outlier: 8.865A pdb=" N ILE B 88 " --> pdb=" O ASP B 296 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS B 298 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N PHE B 90 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLU B 300 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 299 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE B 272 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 208 through 210 removed outlier: 3.994A pdb=" N LEU B 209 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE B 238 " --> pdb=" O LEU B 209 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 227 through 230 Processing sheet with id= D, first strand: chain 'A' and resid 158 through 163 Processing sheet with id= E, first strand: chain 'A' and resid 180 through 183 removed outlier: 3.823A pdb=" N THR A 243 " --> pdb=" O HIS A 199 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS A 199 " --> pdb=" O THR A 243 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 346 through 348 removed outlier: 3.935A pdb=" N ILE A 720 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 704 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET A 724 " --> pdb=" O GLY A 706 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR A 362 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N THR A 705 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS A 364 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS A 602 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N SER A 365 " --> pdb=" O LYS A 602 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE A 604 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 386 through 389 removed outlier: 3.536A pdb=" N HIS A 380 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP A 382 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE A 545 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU A 578 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU A 543 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 480 " --> pdb=" O ILE A 470 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A 468 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 516 through 519 removed outlier: 6.981A pdb=" N LEU A 573 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE A 511 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE A 575 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU A 513 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 652 through 655 removed outlier: 6.504A pdb=" N GLU A 677 " --> pdb=" O CYS A 653 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ILE A 655 " --> pdb=" O GLU A 677 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL A 679 " --> pdb=" O ILE A 655 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 192 through 195 removed outlier: 6.007A pdb=" N ARG A 194 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N VAL A 248 " --> pdb=" O ARG A 194 " (cutoff:3.500A) 374 hydrogen bonds defined for protein. 1071 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: 3.31 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3338 1.35 - 1.47: 2328 1.47 - 1.59: 4667 1.59 - 1.71: 1 1.71 - 1.82: 94 Bond restraints: 10428 Sorted by residual: bond pdb=" CB PRO A 519 " pdb=" CG PRO A 519 " ideal model delta sigma weight residual 1.492 1.615 -0.123 5.00e-02 4.00e+02 6.05e+00 bond pdb=" F3 MF4 A2101 " pdb="MG MF4 A2101 " ideal model delta sigma weight residual 1.837 1.788 0.049 2.00e-02 2.50e+03 6.05e+00 bond pdb=" F2 MF4 A2101 " pdb="MG MF4 A2101 " ideal model delta sigma weight residual 1.836 1.788 0.048 2.00e-02 2.50e+03 5.82e+00 bond pdb=" F1 MF4 A2101 " pdb="MG MF4 A2101 " ideal model delta sigma weight residual 1.836 1.789 0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" F4 MF4 A2101 " pdb="MG MF4 A2101 " ideal model delta sigma weight residual 1.836 1.789 0.047 2.00e-02 2.50e+03 5.50e+00 ... (remaining 10423 not shown) Histogram of bond angle deviations from ideal: 74.99 - 86.91: 1 86.91 - 98.83: 2 98.83 - 110.75: 3400 110.75 - 122.68: 9740 122.68 - 134.60: 988 Bond angle restraints: 14131 Sorted by residual: angle pdb=" N TYR G 32 " pdb=" CA TYR G 32 " pdb=" C TYR G 32 " ideal model delta sigma weight residual 108.20 74.99 33.21 1.71e+00 3.42e-01 3.77e+02 angle pdb=" C TYR G 32 " pdb=" CA TYR G 32 " pdb=" CB TYR G 32 " ideal model delta sigma weight residual 110.78 91.27 19.51 1.60e+00 3.91e-01 1.49e+02 angle pdb=" N ASP G 33 " pdb=" CA ASP G 33 " pdb=" C ASP G 33 " ideal model delta sigma weight residual 110.80 126.71 -15.91 2.13e+00 2.20e-01 5.58e+01 angle pdb=" CA PRO A 983 " pdb=" N PRO A 983 " pdb=" CD PRO A 983 " ideal model delta sigma weight residual 112.00 102.85 9.15 1.40e+00 5.10e-01 4.27e+01 angle pdb=" CA PRO A 519 " pdb=" N PRO A 519 " pdb=" CD PRO A 519 " ideal model delta sigma weight residual 112.00 103.32 8.68 1.40e+00 5.10e-01 3.84e+01 ... (remaining 14126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5603 17.99 - 35.98: 558 35.98 - 53.98: 96 53.98 - 71.97: 17 71.97 - 89.96: 9 Dihedral angle restraints: 6283 sinusoidal: 2530 harmonic: 3753 Sorted by residual: dihedral pdb=" C TYR G 32 " pdb=" N TYR G 32 " pdb=" CA TYR G 32 " pdb=" CB TYR G 32 " ideal model delta harmonic sigma weight residual -122.60 -85.73 -36.87 0 2.50e+00 1.60e-01 2.17e+02 dihedral pdb=" N ASP G 33 " pdb=" C ASP G 33 " pdb=" CA ASP G 33 " pdb=" CB ASP G 33 " ideal model delta harmonic sigma weight residual 122.80 154.71 -31.91 0 2.50e+00 1.60e-01 1.63e+02 dihedral pdb=" C ASP G 33 " pdb=" N ASP G 33 " pdb=" CA ASP G 33 " pdb=" CB ASP G 33 " ideal model delta harmonic sigma weight residual -122.60 -152.40 29.80 0 2.50e+00 1.60e-01 1.42e+02 ... (remaining 6280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.283: 1596 0.283 - 0.565: 1 0.565 - 0.848: 0 0.848 - 1.130: 0 1.130 - 1.413: 1 Chirality restraints: 1598 Sorted by residual: chirality pdb=" CA ASP G 33 " pdb=" N ASP G 33 " pdb=" C ASP G 33 " pdb=" CB ASP G 33 " both_signs ideal model delta sigma weight residual False 2.51 1.10 1.41 2.00e-01 2.50e+01 4.99e+01 chirality pdb=" CA TYR G 32 " pdb=" N TYR G 32 " pdb=" C TYR G 32 " pdb=" CB TYR G 32 " both_signs ideal model delta sigma weight residual False 2.51 3.05 -0.54 2.00e-01 2.50e+01 7.38e+00 chirality pdb=" CA PRO A 983 " pdb=" N PRO A 983 " pdb=" C PRO A 983 " pdb=" CB PRO A 983 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.57e-01 ... (remaining 1595 not shown) Planarity restraints: 1824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 982 " -0.073 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO A 983 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO A 983 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 983 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 825 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.76e+00 pdb=" N PRO A 826 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 826 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 826 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 71 " 0.174 9.50e-02 1.11e+02 7.79e-02 3.73e+00 pdb=" NE ARG B 71 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 71 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 71 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 71 " 0.006 2.00e-02 2.50e+03 ... (remaining 1821 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 5 2.17 - 2.86: 3643 2.86 - 3.54: 14906 3.54 - 4.22: 22548 4.22 - 4.90: 39486 Nonbonded interactions: 80588 Sorted by model distance: nonbonded pdb=" CZ PHE A 90 " pdb=" CG1 VAL A 322 " model vdw 1.492 3.760 nonbonded pdb=" O GLU B 165 " pdb=" OG1 THR B 166 " model vdw 1.982 2.440 nonbonded pdb=" CE1 PHE A 90 " pdb=" CG1 VAL A 322 " model vdw 2.051 3.760 nonbonded pdb=" O SER A 91 " pdb=" N LEU A 94 " model vdw 2.058 2.520 nonbonded pdb=" O SER A 91 " pdb=" N LEU A 93 " model vdw 2.080 2.520 ... (remaining 80583 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.020 Extract box with map and model: 4.320 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.030 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.003 0.123 10428 Z= 0.204 Angle : 0.693 33.213 14131 Z= 0.382 Chirality : 0.056 1.413 1598 Planarity : 0.005 0.105 1824 Dihedral : 14.473 89.962 3866 Min Nonbonded Distance : 1.492 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.39 % Favored : 95.30 % Rotamer: Outliers : 0.27 % Allowed : 0.71 % Favored : 99.02 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 1.61 % 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: -0.48 (0.23), residues: 1299 helix: 0.87 (0.23), residues: 537 sheet: -1.53 (0.40), residues: 150 loop : -1.04 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 896 HIS 0.010 0.001 HIS A 413 PHE 0.021 0.001 PHE A 136 TYR 0.012 0.001 TYR G 34 ARG 0.004 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 197 time to evaluate : 1.307 Fit side-chains REVERT: B 41 ILE cc_start: 0.7865 (tt) cc_final: 0.7617 (tt) REVERT: A 215 GLN cc_start: 0.7439 (mm110) cc_final: 0.7064 (mm110) REVERT: A 360 THR cc_start: 0.8891 (p) cc_final: 0.8671 (p) REVERT: A 409 VAL cc_start: 0.8641 (m) cc_final: 0.8209 (t) REVERT: A 419 ASN cc_start: 0.7179 (m110) cc_final: 0.6794 (m-40) REVERT: A 457 VAL cc_start: 0.8729 (t) cc_final: 0.8124 (m) REVERT: A 724 MET cc_start: 0.8665 (mmt) cc_final: 0.8244 (mmt) outliers start: 3 outliers final: 1 residues processed: 200 average time/residue: 0.1742 time to fit residues: 52.9493 Evaluate side-chains 147 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.0370 chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 118 optimal weight: 2.9990 overall best weight: 1.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN A 464 ASN A 518 GLN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 932 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.0583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10428 Z= 0.167 Angle : 0.500 7.164 14131 Z= 0.261 Chirality : 0.040 0.142 1598 Planarity : 0.004 0.049 1824 Dihedral : 3.956 21.315 1404 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.33 (0.23), residues: 1299 helix: 0.99 (0.23), residues: 541 sheet: -1.30 (0.39), residues: 157 loop : -1.00 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 896 HIS 0.004 0.001 HIS G 31 PHE 0.037 0.001 PHE A 90 TYR 0.017 0.001 TYR G 32 ARG 0.003 0.000 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.239 Fit side-chains REVERT: B 41 ILE cc_start: 0.7847 (tt) cc_final: 0.7578 (tt) REVERT: A 215 GLN cc_start: 0.7428 (mm110) cc_final: 0.7046 (mm110) REVERT: A 409 VAL cc_start: 0.8670 (m) cc_final: 0.8253 (t) REVERT: A 419 ASN cc_start: 0.7164 (m-40) cc_final: 0.6735 (m-40) REVERT: A 460 MET cc_start: 0.8255 (mmp) cc_final: 0.7885 (tpt) REVERT: A 865 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8834 (mm-30) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1706 time to fit residues: 51.0066 Evaluate side-chains 143 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 10428 Z= 0.351 Angle : 0.629 7.729 14131 Z= 0.326 Chirality : 0.044 0.151 1598 Planarity : 0.004 0.045 1824 Dihedral : 4.465 25.621 1404 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.09 % Allowed : 5.62 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.80 (0.23), residues: 1299 helix: 0.47 (0.22), residues: 556 sheet: -1.55 (0.40), residues: 145 loop : -1.18 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 307 HIS 0.012 0.002 HIS A 909 PHE 0.036 0.002 PHE A 90 TYR 0.016 0.002 TYR G 32 ARG 0.003 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 1.719 Fit side-chains REVERT: A 31 MET cc_start: 0.7778 (tmm) cc_final: 0.7547 (tmm) REVERT: A 44 LYS cc_start: 0.7409 (ptmt) cc_final: 0.7095 (ptmt) REVERT: A 215 GLN cc_start: 0.7532 (mm110) cc_final: 0.7155 (mm110) REVERT: A 360 THR cc_start: 0.9150 (p) cc_final: 0.8832 (p) REVERT: A 419 ASN cc_start: 0.7086 (m-40) cc_final: 0.6779 (m110) outliers start: 1 outliers final: 1 residues processed: 199 average time/residue: 0.1892 time to fit residues: 56.5344 Evaluate side-chains 148 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10428 Z= 0.230 Angle : 0.553 7.228 14131 Z= 0.285 Chirality : 0.041 0.141 1598 Planarity : 0.004 0.062 1824 Dihedral : 4.327 24.119 1404 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.69 (0.23), residues: 1299 helix: 0.64 (0.22), residues: 549 sheet: -1.41 (0.39), residues: 153 loop : -1.19 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 896 HIS 0.004 0.001 HIS A 909 PHE 0.027 0.001 PHE A 423 TYR 0.011 0.001 TYR B 204 ARG 0.005 0.000 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.204 Fit side-chains revert: symmetry clash REVERT: B 41 ILE cc_start: 0.7943 (tt) cc_final: 0.7701 (tt) REVERT: B 165 GLU cc_start: 0.6426 (mt-10) cc_final: 0.6167 (mp0) REVERT: B 202 MET cc_start: 0.3791 (tpt) cc_final: 0.3171 (ttt) REVERT: A 215 GLN cc_start: 0.7539 (mm110) cc_final: 0.7172 (mm110) REVERT: A 355 GLU cc_start: 0.8331 (tp30) cc_final: 0.8078 (tp30) REVERT: A 419 ASN cc_start: 0.7092 (m-40) cc_final: 0.6820 (m110) REVERT: A 460 MET cc_start: 0.8264 (mmp) cc_final: 0.7958 (tpt) REVERT: A 859 TYR cc_start: 0.9129 (t80) cc_final: 0.8861 (t80) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1944 time to fit residues: 57.0600 Evaluate side-chains 149 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 93 optimal weight: 0.4980 chunk 51 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10428 Z= 0.179 Angle : 0.530 7.001 14131 Z= 0.273 Chirality : 0.040 0.141 1598 Planarity : 0.004 0.056 1824 Dihedral : 4.185 23.263 1404 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.57 (0.23), residues: 1299 helix: 0.72 (0.22), residues: 550 sheet: -1.28 (0.40), residues: 152 loop : -1.13 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 155 HIS 0.003 0.001 HIS A 547 PHE 0.023 0.001 PHE A 423 TYR 0.021 0.001 TYR B 204 ARG 0.005 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.292 Fit side-chains REVERT: B 41 ILE cc_start: 0.7893 (tt) cc_final: 0.7660 (tt) REVERT: A 215 GLN cc_start: 0.7524 (mm110) cc_final: 0.7150 (mm110) REVERT: A 324 GLU cc_start: 0.7786 (mp0) cc_final: 0.7515 (mp0) REVERT: A 355 GLU cc_start: 0.8243 (tp30) cc_final: 0.8014 (tp30) REVERT: A 360 THR cc_start: 0.9126 (p) cc_final: 0.8925 (p) REVERT: A 460 MET cc_start: 0.8271 (mmp) cc_final: 0.7930 (tpt) REVERT: A 859 TYR cc_start: 0.9193 (t80) cc_final: 0.8762 (t80) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1879 time to fit residues: 56.2596 Evaluate side-chains 150 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 125 optimal weight: 0.0170 chunk 104 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN A 419 ASN A 464 ASN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10428 Z= 0.186 Angle : 0.542 7.029 14131 Z= 0.280 Chirality : 0.041 0.152 1598 Planarity : 0.004 0.043 1824 Dihedral : 4.185 25.684 1404 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.56 (0.23), residues: 1299 helix: 0.77 (0.23), residues: 547 sheet: -1.33 (0.40), residues: 145 loop : -1.16 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 155 HIS 0.003 0.001 HIS A 547 PHE 0.028 0.001 PHE A 90 TYR 0.016 0.001 TYR B 204 ARG 0.003 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.260 Fit side-chains REVERT: B 41 ILE cc_start: 0.7889 (tt) cc_final: 0.7656 (tt) REVERT: B 202 MET cc_start: 0.3518 (tpt) cc_final: 0.2985 (ttt) REVERT: A 215 GLN cc_start: 0.7498 (mm110) cc_final: 0.7145 (mm110) REVERT: A 324 GLU cc_start: 0.7750 (mp0) cc_final: 0.7533 (mp0) REVERT: A 355 GLU cc_start: 0.8182 (tp30) cc_final: 0.7951 (tp30) REVERT: A 460 MET cc_start: 0.8209 (mmp) cc_final: 0.7920 (tpt) REVERT: A 724 MET cc_start: 0.8664 (mmm) cc_final: 0.8375 (mmt) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1798 time to fit residues: 53.9399 Evaluate side-chains 142 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 10428 Z= 0.388 Angle : 0.671 7.556 14131 Z= 0.349 Chirality : 0.045 0.143 1598 Planarity : 0.005 0.057 1824 Dihedral : 4.719 27.354 1404 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.23), residues: 1299 helix: 0.28 (0.22), residues: 558 sheet: -1.73 (0.39), residues: 140 loop : -1.23 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 307 HIS 0.007 0.002 HIS A 909 PHE 0.042 0.002 PHE A 90 TYR 0.022 0.002 TYR B 204 ARG 0.008 0.001 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.282 Fit side-chains REVERT: A 44 LYS cc_start: 0.7432 (ptmt) cc_final: 0.7008 (ptmt) REVERT: A 136 PHE cc_start: 0.8661 (t80) cc_final: 0.8363 (t80) REVERT: A 215 GLN cc_start: 0.7479 (mm110) cc_final: 0.7169 (mm110) REVERT: A 724 MET cc_start: 0.8652 (mmm) cc_final: 0.8141 (mmt) REVERT: A 782 LEU cc_start: 0.8293 (mt) cc_final: 0.8059 (mt) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1801 time to fit residues: 53.2490 Evaluate side-chains 149 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 chunk 98 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 419 ASN A 464 ASN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 866 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10428 Z= 0.172 Angle : 0.573 6.947 14131 Z= 0.292 Chirality : 0.041 0.160 1598 Planarity : 0.004 0.044 1824 Dihedral : 4.353 26.719 1404 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.67 (0.23), residues: 1299 helix: 0.62 (0.22), residues: 555 sheet: -1.37 (0.40), residues: 144 loop : -1.17 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 977 HIS 0.003 0.001 HIS A 547 PHE 0.027 0.001 PHE A 90 TYR 0.016 0.001 TYR A 768 ARG 0.003 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.203 Fit side-chains REVERT: A 136 PHE cc_start: 0.8490 (t80) cc_final: 0.8164 (t80) REVERT: A 215 GLN cc_start: 0.7503 (mm110) cc_final: 0.7156 (mm-40) REVERT: A 440 ASP cc_start: 0.6797 (t0) cc_final: 0.6595 (t0) REVERT: A 460 MET cc_start: 0.8290 (mmp) cc_final: 0.7898 (tpt) REVERT: A 639 ASN cc_start: 0.7695 (p0) cc_final: 0.7377 (p0) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1881 time to fit residues: 53.8284 Evaluate side-chains 145 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 0.0980 chunk 76 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN A 464 ASN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10428 Z= 0.175 Angle : 0.555 7.062 14131 Z= 0.283 Chirality : 0.041 0.146 1598 Planarity : 0.004 0.044 1824 Dihedral : 4.223 24.577 1404 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.51 (0.23), residues: 1299 helix: 0.71 (0.22), residues: 555 sheet: -1.13 (0.40), residues: 151 loop : -1.09 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 896 HIS 0.004 0.001 HIS A 380 PHE 0.023 0.001 PHE A 90 TYR 0.014 0.001 TYR B 204 ARG 0.003 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.218 Fit side-chains REVERT: B 41 ILE cc_start: 0.7820 (tt) cc_final: 0.7608 (tt) REVERT: B 202 MET cc_start: 0.3948 (tpt) cc_final: 0.3346 (ttt) REVERT: A 136 PHE cc_start: 0.8496 (t80) cc_final: 0.8165 (t80) REVERT: A 215 GLN cc_start: 0.7499 (mm110) cc_final: 0.7136 (mm110) REVERT: A 457 VAL cc_start: 0.8910 (t) cc_final: 0.8640 (m) REVERT: A 460 MET cc_start: 0.8284 (mmp) cc_final: 0.7901 (tpt) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1791 time to fit residues: 53.1287 Evaluate side-chains 149 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 85 optimal weight: 0.0040 chunk 129 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 overall best weight: 1.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 HIS ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10428 Z= 0.226 Angle : 0.579 7.417 14131 Z= 0.296 Chirality : 0.041 0.149 1598 Planarity : 0.004 0.045 1824 Dihedral : 4.289 24.238 1404 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.58 (0.23), residues: 1299 helix: 0.66 (0.22), residues: 556 sheet: -1.21 (0.41), residues: 149 loop : -1.12 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 896 HIS 0.004 0.001 HIS A 909 PHE 0.027 0.001 PHE A 90 TYR 0.016 0.001 TYR B 204 ARG 0.003 0.000 ARG A 375 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.319 Fit side-chains REVERT: B 41 ILE cc_start: 0.7812 (tt) cc_final: 0.7568 (tt) REVERT: B 165 GLU cc_start: 0.6441 (pt0) cc_final: 0.5757 (mp0) REVERT: B 202 MET cc_start: 0.4109 (tpt) cc_final: 0.3449 (ttt) REVERT: A 136 PHE cc_start: 0.8563 (t80) cc_final: 0.8246 (t80) REVERT: A 215 GLN cc_start: 0.7478 (mm110) cc_final: 0.7143 (mm110) REVERT: A 457 VAL cc_start: 0.8897 (t) cc_final: 0.8668 (m) REVERT: A 460 MET cc_start: 0.8274 (mmp) cc_final: 0.7902 (tpt) REVERT: A 859 TYR cc_start: 0.9065 (t80) cc_final: 0.8852 (t80) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1779 time to fit residues: 52.8110 Evaluate side-chains 147 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 43 optimal weight: 0.0870 chunk 106 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 5 optimal weight: 0.0770 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 419 ASN A 464 ASN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.131245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103599 restraints weight = 18888.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106164 restraints weight = 11152.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107913 restraints weight = 7649.464| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10428 Z= 0.173 Angle : 0.550 7.078 14131 Z= 0.279 Chirality : 0.041 0.154 1598 Planarity : 0.004 0.045 1824 Dihedral : 4.187 23.312 1404 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.54 (0.23), residues: 1299 helix: 0.65 (0.23), residues: 566 sheet: -1.20 (0.41), residues: 148 loop : -1.08 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 896 HIS 0.003 0.001 HIS A 547 PHE 0.023 0.001 PHE A 90 TYR 0.014 0.001 TYR B 204 ARG 0.003 0.000 ARG A 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2140.47 seconds wall clock time: 39 minutes 45.33 seconds (2385.33 seconds total)