Starting phenix.real_space_refine on Mon Jul 28 11:56:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8se9_40407/07_2025/8se9_40407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8se9_40407/07_2025/8se9_40407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8se9_40407/07_2025/8se9_40407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8se9_40407/07_2025/8se9_40407.map" model { file = "/net/cci-nas-00/data/ceres_data/8se9_40407/07_2025/8se9_40407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8se9_40407/07_2025/8se9_40407.cif" } resolution = 3.2 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 38 5.16 5 C 6480 2.51 5 N 1790 2.21 5 O 1886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10195 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7693 Classifications: {'peptide': 989} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 923} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 633 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "C" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1243 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 133} Chain: "D" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 7.07, per 1000 atoms: 0.69 Number of scatterers: 10195 At special positions: 0 Unit cell: (91.652, 105.816, 117.481, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 1 15.00 O 1886 8.00 N 1790 7.00 C 6480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS C 86 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 10 sheets defined 44.3% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 24 through 31 removed outlier: 3.533A pdb=" N ARG A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 31 " --> pdb=" O MET A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 55 Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.909A pdb=" N ASP A 71 " --> pdb=" O CYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 86 through 99 removed outlier: 3.919A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 119 removed outlier: 3.837A pdb=" N ASP A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 142 Processing helix chain 'A' and resid 197 through 203 removed outlier: 4.268A pdb=" N HIS A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 280 through 305 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 342 through 352 Processing helix chain 'A' and resid 357 through 378 Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.528A pdb=" N CYS A 394 " --> pdb=" O ALA A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 423 through 432 Processing helix chain 'A' and resid 441 through 455 Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.921A pdb=" N ARG A 479 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 480 " --> pdb=" O LEU A 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 476 through 480' Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.557A pdb=" N ASP A 487 " --> pdb=" O ARG A 484 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 488 " --> pdb=" O SER A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 488' Processing helix chain 'A' and resid 491 through 504 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.835A pdb=" N GLU A 521 " --> pdb=" O PRO A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 541 through 556 Processing helix chain 'A' and resid 585 through 593 removed outlier: 4.359A pdb=" N ASP A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 601 removed outlier: 3.602A pdb=" N THR A 600 " --> pdb=" O PRO A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 624 Processing helix chain 'A' and resid 624 through 631 removed outlier: 4.043A pdb=" N GLU A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASN A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 644 through 653 removed outlier: 4.302A pdb=" N THR A 648 " --> pdb=" O ASP A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 682 removed outlier: 4.771A pdb=" N HIS A 676 " --> pdb=" O TRP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 722 through 740 removed outlier: 3.638A pdb=" N TYR A 727 " --> pdb=" O THR A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 756 Processing helix chain 'A' and resid 760 through 763 removed outlier: 3.512A pdb=" N GLN A 763 " --> pdb=" O PRO A 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 760 through 763' Processing helix chain 'A' and resid 764 through 770 removed outlier: 3.611A pdb=" N ILE A 768 " --> pdb=" O GLN A 764 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 798 Processing helix chain 'A' and resid 816 through 832 removed outlier: 3.553A pdb=" N PHE A 820 " --> pdb=" O PHE A 816 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 821 " --> pdb=" O HIS A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 844 Processing helix chain 'A' and resid 853 through 874 removed outlier: 3.678A pdb=" N LYS A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 881 Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing helix chain 'A' and resid 927 through 939 Processing helix chain 'A' and resid 959 through 967 Processing helix chain 'A' and resid 970 through 980 Processing helix chain 'B' and resid 103 through 116 removed outlier: 3.589A pdb=" N LEU B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 141 removed outlier: 3.605A pdb=" N GLY B 141 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 17 removed outlier: 3.616A pdb=" N LYS C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS C 17 " --> pdb=" O ASP C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.610A pdb=" N LEU C 48 " --> pdb=" O PRO C 45 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS C 49 " --> pdb=" O TYR C 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 49' Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.642A pdb=" N VAL C 104 " --> pdb=" O LYS C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 132 through 148 Processing helix chain 'D' and resid 103 through 116 removed outlier: 4.677A pdb=" N GLN D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 141 removed outlier: 3.991A pdb=" N GLU D 139 " --> pdb=" O PRO D 136 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY D 141 " --> pdb=" O GLY D 138 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 7.869A pdb=" N HIS A 62 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A 37 " --> pdb=" O HIS A 62 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU A 36 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 152 removed outlier: 3.630A pdb=" N VAL A 155 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.404A pdb=" N LEU A 208 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 254 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS A 183 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 509 through 512 removed outlier: 6.853A pdb=" N LEU A 464 " --> pdb=" O ILE A 510 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU A 512 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 466 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 437 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 559 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 904 through 906 Processing sheet with id=AA7, first strand: chain 'A' and resid 917 through 920 removed outlier: 6.354A pdb=" N LEU A 917 " --> pdb=" O HIS A1009 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU A1011 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 919 " --> pdb=" O GLU A1011 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE A 945 " --> pdb=" O SER A 995 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ARG A 944 " --> pdb=" O ALA A 955 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA A 955 " --> pdb=" O ARG A 944 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU A 946 " --> pdb=" O LEU A 953 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 95 removed outlier: 6.689A pdb=" N LEU B 85 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N MET B 150 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG B 87 " --> pdb=" O MET B 150 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU B 152 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 26 removed outlier: 6.025A pdb=" N ASN C 24 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU C 38 " --> pdb=" O ASN C 24 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 85 through 86 removed outlier: 7.757A pdb=" N LEU D 85 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N MET D 150 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN D 151 " --> pdb=" O TRP D 123 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TRP D 123 " --> pdb=" O ASN D 151 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1146 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: 3.56 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3379 1.34 - 1.46: 1342 1.46 - 1.57: 5665 1.57 - 1.69: 4 1.69 - 1.81: 57 Bond restraints: 10447 Sorted by residual: bond pdb=" C1' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 1.426 1.624 -0.198 2.00e-02 2.50e+03 9.77e+01 bond pdb=" C1' AMP B1101 " pdb=" C2' AMP B1101 " ideal model delta sigma weight residual 1.524 1.363 0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" C6 AMP B1101 " pdb=" N6 AMP B1101 " ideal model delta sigma weight residual 1.355 1.499 -0.144 2.00e-02 2.50e+03 5.15e+01 bond pdb=" C4' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 1.426 1.294 0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" C4 AMP B1101 " pdb=" C5 AMP B1101 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.30e+01 ... (remaining 10442 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 14179 3.39 - 6.78: 38 6.78 - 10.18: 2 10.18 - 13.57: 3 13.57 - 16.96: 2 Bond angle restraints: 14224 Sorted by residual: angle pdb=" C2' AMP B1101 " pdb=" C1' AMP B1101 " pdb=" N9 AMP B1101 " ideal model delta sigma weight residual 109.47 126.43 -16.96 3.00e+00 1.11e-01 3.20e+01 angle pdb=" N9 AMP B1101 " pdb=" C1' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 109.47 94.58 14.89 3.00e+00 1.11e-01 2.46e+01 angle pdb=" O2P AMP B1101 " pdb=" P AMP B1101 " pdb=" O3P AMP B1101 " ideal model delta sigma weight residual 119.90 106.91 12.99 3.00e+00 1.11e-01 1.87e+01 angle pdb=" C GLY A 187 " pdb=" N SER A 188 " pdb=" CA SER A 188 " ideal model delta sigma weight residual 121.80 132.20 -10.40 2.44e+00 1.68e-01 1.82e+01 angle pdb=" O1P AMP B1101 " pdb=" P AMP B1101 " pdb=" O2P AMP B1101 " ideal model delta sigma weight residual 119.60 106.93 12.67 3.00e+00 1.11e-01 1.78e+01 ... (remaining 14219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 5886 17.67 - 35.35: 322 35.35 - 53.02: 65 53.02 - 70.70: 14 70.70 - 88.37: 8 Dihedral angle restraints: 6295 sinusoidal: 2548 harmonic: 3747 Sorted by residual: dihedral pdb=" CA SER A 188 " pdb=" C SER A 188 " pdb=" N PRO A 189 " pdb=" CA PRO A 189 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA GLN A 923 " pdb=" C GLN A 923 " pdb=" N PRO A 924 " pdb=" CA PRO A 924 " 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=" CA GLN A 385 " pdb=" C GLN A 385 " pdb=" N TRP A 386 " pdb=" CA TRP A 386 " ideal model delta harmonic sigma weight residual -180.00 -164.56 -15.44 0 5.00e+00 4.00e-02 9.53e+00 ... (remaining 6292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 987 0.029 - 0.058: 416 0.058 - 0.087: 105 0.087 - 0.116: 69 0.116 - 0.145: 11 Chirality restraints: 1588 Sorted by residual: chirality pdb=" C3' AMP B1101 " pdb=" C2' AMP B1101 " pdb=" C4' AMP B1101 " pdb=" O3' AMP B1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.14 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" C2' AMP B1101 " pdb=" C1' AMP B1101 " pdb=" C3' AMP B1101 " pdb=" O2' AMP B1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.37 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE A 945 " pdb=" N ILE A 945 " pdb=" C ILE A 945 " pdb=" CB ILE A 945 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1585 not shown) Planarity restraints: 1865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 517 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO A 518 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 188 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO A 189 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 923 " -0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO A 924 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 924 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 924 " -0.015 5.00e-02 4.00e+02 ... (remaining 1862 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 941 2.74 - 3.28: 10079 3.28 - 3.82: 16340 3.82 - 4.36: 18988 4.36 - 4.90: 33477 Nonbonded interactions: 79825 Sorted by model distance: nonbonded pdb=" OE1 GLU A 925 " pdb=" OG1 THR A 972 " model vdw 2.204 3.040 nonbonded pdb=" O TYR A 514 " pdb=" OH TYR A 524 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR C 46 " pdb=" O TYR C 75 " model vdw 2.235 3.040 nonbonded pdb=" OD1 ASP A 468 " pdb=" O2' AMP B1101 " model vdw 2.239 3.040 nonbonded pdb=" NE2 GLN C 15 " pdb=" O LEU C 25 " model vdw 2.289 3.120 ... (remaining 79820 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 'B' and resid 82 through 157) selection = chain 'D' } 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.630 Find NCS groups from input model: 0.140 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 : 0.005 0.198 10450 Z= 0.260 Angle : 0.592 16.960 14226 Z= 0.271 Chirality : 0.038 0.145 1588 Planarity : 0.004 0.048 1865 Dihedral : 11.993 88.369 3868 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.41 % Favored : 96.43 % Rotamer: Outliers : 2.00 % Allowed : 7.45 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.24), residues: 1289 helix: 1.53 (0.24), residues: 457 sheet: -0.62 (0.40), residues: 171 loop : -0.21 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 95 HIS 0.002 0.001 HIS A 275 PHE 0.008 0.001 PHE A 146 TYR 0.008 0.001 TYR C 61 ARG 0.002 0.000 ARG C 118 Details of bonding type rmsd hydrogen bonds : bond 0.16395 ( 411) hydrogen bonds : angle 6.83715 ( 1146) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.71986 ( 2) covalent geometry : bond 0.00485 (10447) covalent geometry : angle 0.59229 (14224) Misc. bond : bond 0.08991 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8696 (mp) REVERT: A 225 PRO cc_start: 0.8058 (Cg_exo) cc_final: 0.7802 (Cg_endo) REVERT: A 273 GLN cc_start: 0.7357 (tm-30) cc_final: 0.6963 (tm-30) REVERT: A 373 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8519 (mm) REVERT: A 508 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7171 (mt0) REVERT: A 531 ARG cc_start: 0.7921 (mtm110) cc_final: 0.7513 (ptp-110) REVERT: A 638 THR cc_start: 0.3737 (OUTLIER) cc_final: 0.3269 (m) REVERT: A 738 MET cc_start: 0.3515 (ppp) cc_final: 0.0512 (mmm) REVERT: C 5 MET cc_start: 0.8894 (tpt) cc_final: 0.8506 (tpt) REVERT: C 43 GLN cc_start: 0.7700 (tm-30) cc_final: 0.7496 (tm-30) REVERT: C 70 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8005 (m-80) REVERT: D 99 ARG cc_start: 0.8030 (mmp-170) cc_final: 0.7529 (mmm160) outliers start: 22 outliers final: 10 residues processed: 152 average time/residue: 0.2441 time to fit residues: 51.2617 Evaluate side-chains 120 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 116 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 140 HIS A 199 ASN A 634 GLN A 637 HIS A 786 GLN A 817 HIS A 939 HIS A1009 HIS B 106 HIS B 110 GLN C 103 GLN D 106 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.199835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.125543 restraints weight = 12382.087| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.38 r_work: 0.3268 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10450 Z= 0.161 Angle : 0.590 10.383 14226 Z= 0.284 Chirality : 0.040 0.127 1588 Planarity : 0.004 0.055 1865 Dihedral : 6.094 58.877 1432 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.03 % Favored : 96.90 % Rotamer: Outliers : 2.45 % Allowed : 10.45 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.35 (0.24), residues: 1289 helix: 1.47 (0.24), residues: 468 sheet: -0.67 (0.40), residues: 170 loop : -0.37 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 677 HIS 0.007 0.001 HIS A 682 PHE 0.014 0.001 PHE A 481 TYR 0.013 0.001 TYR B 140 ARG 0.005 0.000 ARG A 258 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 411) hydrogen bonds : angle 5.30934 ( 1146) SS BOND : bond 0.00235 ( 1) SS BOND : angle 0.49245 ( 2) covalent geometry : bond 0.00389 (10447) covalent geometry : angle 0.58989 (14224) Misc. bond : bond 0.00589 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8775 (mp) REVERT: A 225 PRO cc_start: 0.8390 (Cg_exo) cc_final: 0.8162 (Cg_endo) REVERT: A 273 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7421 (tm-30) REVERT: A 508 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7297 (mt0) REVERT: A 531 ARG cc_start: 0.8016 (mtm110) cc_final: 0.7684 (ptp-110) REVERT: A 638 THR cc_start: 0.4069 (OUTLIER) cc_final: 0.3833 (m) REVERT: A 738 MET cc_start: 0.3867 (ppp) cc_final: 0.1031 (mmm) REVERT: C 5 MET cc_start: 0.8886 (tpt) cc_final: 0.8482 (tpt) REVERT: C 13 ASP cc_start: 0.8088 (t0) cc_final: 0.7881 (m-30) REVERT: C 43 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7564 (tm-30) REVERT: C 70 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: D 99 ARG cc_start: 0.8282 (mmp-170) cc_final: 0.7701 (mmm160) REVERT: D 110 GLN cc_start: 0.1998 (OUTLIER) cc_final: 0.1623 (mp10) outliers start: 27 outliers final: 13 residues processed: 132 average time/residue: 0.2427 time to fit residues: 45.1640 Evaluate side-chains 124 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 104 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 10 optimal weight: 0.0170 chunk 71 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 HIS A 908 HIS ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.200427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.125811 restraints weight = 12579.514| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.21 r_work: 0.3313 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10450 Z= 0.113 Angle : 0.546 10.357 14226 Z= 0.258 Chirality : 0.039 0.126 1588 Planarity : 0.004 0.054 1865 Dihedral : 5.785 59.391 1428 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.05 % Rotamer: Outliers : 2.00 % Allowed : 12.09 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.44 (0.24), residues: 1289 helix: 1.59 (0.24), residues: 468 sheet: -0.67 (0.40), residues: 164 loop : -0.35 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 677 HIS 0.004 0.001 HIS A 682 PHE 0.013 0.001 PHE A 481 TYR 0.007 0.001 TYR A 547 ARG 0.005 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 411) hydrogen bonds : angle 4.93489 ( 1146) SS BOND : bond 0.00304 ( 1) SS BOND : angle 0.45874 ( 2) covalent geometry : bond 0.00263 (10447) covalent geometry : angle 0.54631 (14224) Misc. bond : bond 0.00028 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8763 (mp) REVERT: A 225 PRO cc_start: 0.8497 (Cg_exo) cc_final: 0.8234 (Cg_endo) REVERT: A 231 ARG cc_start: 0.6677 (ttm170) cc_final: 0.6462 (ttm170) REVERT: A 273 GLN cc_start: 0.7574 (tm-30) cc_final: 0.7338 (tm-30) REVERT: A 373 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8728 (mm) REVERT: A 508 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7468 (pt0) REVERT: A 531 ARG cc_start: 0.7992 (mtm110) cc_final: 0.7679 (ptp-110) REVERT: A 568 TRP cc_start: 0.8771 (m100) cc_final: 0.8508 (m100) REVERT: A 638 THR cc_start: 0.4273 (OUTLIER) cc_final: 0.4040 (m) REVERT: A 738 MET cc_start: 0.3953 (ppp) cc_final: 0.1207 (mmm) REVERT: B 140 TYR cc_start: 0.8067 (m-80) cc_final: 0.7311 (m-10) REVERT: C 5 MET cc_start: 0.8820 (tpt) cc_final: 0.8455 (tpt) REVERT: C 43 GLN cc_start: 0.7778 (tm-30) cc_final: 0.7555 (tm-30) REVERT: C 128 LEU cc_start: 0.8349 (mp) cc_final: 0.8016 (tt) REVERT: D 99 ARG cc_start: 0.8273 (mmp-170) cc_final: 0.7753 (mmm160) REVERT: D 110 GLN cc_start: 0.2008 (OUTLIER) cc_final: 0.1692 (mp10) outliers start: 22 outliers final: 13 residues processed: 128 average time/residue: 0.3336 time to fit residues: 61.0968 Evaluate side-chains 128 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 50 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 82 optimal weight: 0.0470 chunk 2 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 102 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 = 0.4349 r_free = 0.4349 target = 0.199087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.126465 restraints weight = 12504.840| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.43 r_work: 0.3264 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10450 Z= 0.132 Angle : 0.560 10.361 14226 Z= 0.263 Chirality : 0.039 0.182 1588 Planarity : 0.004 0.055 1865 Dihedral : 5.693 59.833 1426 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.82 % Rotamer: Outliers : 2.73 % Allowed : 12.45 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.41 (0.24), residues: 1289 helix: 1.53 (0.24), residues: 473 sheet: -0.69 (0.40), residues: 164 loop : -0.35 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 677 HIS 0.002 0.001 HIS A 291 PHE 0.014 0.001 PHE A 481 TYR 0.008 0.001 TYR A 547 ARG 0.006 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.03294 ( 411) hydrogen bonds : angle 4.82135 ( 1146) SS BOND : bond 0.00220 ( 1) SS BOND : angle 0.31204 ( 2) covalent geometry : bond 0.00321 (10447) covalent geometry : angle 0.55979 (14224) Misc. bond : bond 0.00027 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8828 (mp) REVERT: A 225 PRO cc_start: 0.8512 (Cg_exo) cc_final: 0.8252 (Cg_endo) REVERT: A 231 ARG cc_start: 0.6734 (ttm170) cc_final: 0.6493 (ttm170) REVERT: A 273 GLN cc_start: 0.7701 (tm-30) cc_final: 0.7489 (tm-30) REVERT: A 373 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8789 (mm) REVERT: A 508 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7528 (pt0) REVERT: A 531 ARG cc_start: 0.7999 (mtm110) cc_final: 0.7668 (ptp-110) REVERT: A 568 TRP cc_start: 0.8822 (m100) cc_final: 0.8546 (m100) REVERT: A 610 HIS cc_start: 0.6940 (m90) cc_final: 0.6723 (m90) REVERT: A 638 THR cc_start: 0.4198 (OUTLIER) cc_final: 0.3933 (m) REVERT: A 738 MET cc_start: 0.3931 (ppp) cc_final: 0.1203 (mmm) REVERT: A 864 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8544 (mt) REVERT: C 5 MET cc_start: 0.8838 (tpt) cc_final: 0.8369 (tpt) REVERT: C 25 LEU cc_start: 0.7412 (tp) cc_final: 0.7169 (tp) REVERT: C 43 GLN cc_start: 0.7769 (tm-30) cc_final: 0.7559 (tm-30) REVERT: C 70 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8049 (m-80) REVERT: C 128 LEU cc_start: 0.8289 (mp) cc_final: 0.7899 (tt) REVERT: D 99 ARG cc_start: 0.8261 (mmp-170) cc_final: 0.7733 (mmm160) REVERT: D 110 GLN cc_start: 0.2429 (OUTLIER) cc_final: 0.2226 (mp10) outliers start: 30 outliers final: 16 residues processed: 132 average time/residue: 0.2317 time to fit residues: 43.4109 Evaluate side-chains 130 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 18 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 102 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 = 0.4351 r_free = 0.4351 target = 0.199302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.123672 restraints weight = 12498.386| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.46 r_work: 0.3293 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10450 Z= 0.130 Angle : 0.561 10.368 14226 Z= 0.262 Chirality : 0.039 0.198 1588 Planarity : 0.004 0.054 1865 Dihedral : 5.663 59.439 1426 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 2.55 % Allowed : 12.82 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1289 helix: 1.59 (0.24), residues: 472 sheet: -0.72 (0.40), residues: 164 loop : -0.35 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 677 HIS 0.002 0.001 HIS A 291 PHE 0.015 0.001 PHE A 481 TYR 0.011 0.001 TYR B 140 ARG 0.005 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 411) hydrogen bonds : angle 4.73315 ( 1146) SS BOND : bond 0.00214 ( 1) SS BOND : angle 0.33151 ( 2) covalent geometry : bond 0.00316 (10447) covalent geometry : angle 0.56094 (14224) Misc. bond : bond 0.00034 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 1.807 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8796 (mp) REVERT: A 225 PRO cc_start: 0.8468 (Cg_exo) cc_final: 0.8206 (Cg_endo) REVERT: A 273 GLN cc_start: 0.7575 (tm-30) cc_final: 0.7362 (tm-30) REVERT: A 373 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8743 (mm) REVERT: A 508 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7471 (pt0) REVERT: A 531 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7645 (ptp-110) REVERT: A 568 TRP cc_start: 0.8798 (m100) cc_final: 0.8522 (m100) REVERT: A 638 THR cc_start: 0.4287 (OUTLIER) cc_final: 0.4073 (m) REVERT: A 713 GLN cc_start: 0.9058 (tt0) cc_final: 0.8695 (pp30) REVERT: A 738 MET cc_start: 0.3935 (ppp) cc_final: 0.1258 (mmm) REVERT: A 864 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8529 (mt) REVERT: B 140 TYR cc_start: 0.8000 (m-10) cc_final: 0.7706 (m-10) REVERT: C 5 MET cc_start: 0.8826 (tpt) cc_final: 0.8376 (tpt) REVERT: C 25 LEU cc_start: 0.7372 (tp) cc_final: 0.7137 (tp) REVERT: C 43 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7557 (tm-30) REVERT: C 70 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8068 (m-80) REVERT: C 128 LEU cc_start: 0.8272 (mp) cc_final: 0.7909 (tt) outliers start: 28 outliers final: 15 residues processed: 134 average time/residue: 0.3593 time to fit residues: 70.0836 Evaluate side-chains 128 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 111 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 24 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 124 optimal weight: 0.0970 chunk 77 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN ** D 102 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 = 0.4357 r_free = 0.4357 target = 0.199909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126265 restraints weight = 12485.180| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.35 r_work: 0.3302 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10450 Z= 0.115 Angle : 0.551 10.315 14226 Z= 0.259 Chirality : 0.039 0.172 1588 Planarity : 0.004 0.053 1865 Dihedral : 5.330 59.615 1423 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 2.18 % Allowed : 14.00 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.49 (0.24), residues: 1289 helix: 1.65 (0.24), residues: 472 sheet: -0.71 (0.40), residues: 164 loop : -0.32 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 677 HIS 0.002 0.001 HIS A 610 PHE 0.018 0.001 PHE A 481 TYR 0.013 0.001 TYR C 75 ARG 0.005 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.03060 ( 411) hydrogen bonds : angle 4.61321 ( 1146) SS BOND : bond 0.00220 ( 1) SS BOND : angle 0.30214 ( 2) covalent geometry : bond 0.00277 (10447) covalent geometry : angle 0.55075 (14224) Misc. bond : bond 0.00027 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8797 (mp) REVERT: A 225 PRO cc_start: 0.8472 (Cg_exo) cc_final: 0.8185 (Cg_endo) REVERT: A 273 GLN cc_start: 0.7574 (tm-30) cc_final: 0.7359 (tm-30) REVERT: A 373 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8739 (mm) REVERT: A 469 MET cc_start: 0.7640 (ptp) cc_final: 0.7393 (ptt) REVERT: A 508 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7473 (pt0) REVERT: A 531 ARG cc_start: 0.7983 (mtm110) cc_final: 0.7647 (ptp-110) REVERT: A 568 TRP cc_start: 0.8785 (m100) cc_final: 0.8483 (m100) REVERT: A 738 MET cc_start: 0.3961 (ppp) cc_final: 0.1313 (mmm) REVERT: A 864 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8523 (mt) REVERT: C 25 LEU cc_start: 0.7318 (tp) cc_final: 0.7102 (tp) REVERT: C 43 GLN cc_start: 0.7786 (tm-30) cc_final: 0.7568 (tm-30) REVERT: C 70 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8043 (m-80) REVERT: C 78 ASN cc_start: 0.7265 (m-40) cc_final: 0.6971 (m-40) REVERT: C 128 LEU cc_start: 0.8285 (mp) cc_final: 0.7885 (tt) REVERT: D 99 ARG cc_start: 0.8298 (mmp-170) cc_final: 0.7685 (mmm160) outliers start: 24 outliers final: 15 residues processed: 130 average time/residue: 0.2204 time to fit residues: 40.9340 Evaluate side-chains 127 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 149 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 63 optimal weight: 0.0670 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 115 optimal weight: 0.0020 chunk 123 optimal weight: 0.4980 chunk 114 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.4328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN C 76 HIS ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.200611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.126384 restraints weight = 12574.774| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.40 r_work: 0.3309 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10450 Z= 0.101 Angle : 0.542 10.348 14226 Z= 0.255 Chirality : 0.038 0.163 1588 Planarity : 0.004 0.051 1865 Dihedral : 5.123 58.620 1422 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 1.55 % Allowed : 15.09 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.24), residues: 1289 helix: 1.73 (0.24), residues: 471 sheet: -0.65 (0.40), residues: 164 loop : -0.28 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 677 HIS 0.003 0.000 HIS A 908 PHE 0.009 0.001 PHE A 481 TYR 0.023 0.001 TYR B 140 ARG 0.003 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 411) hydrogen bonds : angle 4.54860 ( 1146) SS BOND : bond 0.00210 ( 1) SS BOND : angle 0.22067 ( 2) covalent geometry : bond 0.00237 (10447) covalent geometry : angle 0.54172 (14224) Misc. bond : bond 0.00021 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8777 (mp) REVERT: A 225 PRO cc_start: 0.8456 (Cg_exo) cc_final: 0.8186 (Cg_endo) REVERT: A 273 GLN cc_start: 0.7558 (tm-30) cc_final: 0.7346 (tm-30) REVERT: A 373 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8701 (mm) REVERT: A 508 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7261 (mt0) REVERT: A 531 ARG cc_start: 0.7992 (mtm110) cc_final: 0.7656 (ptp-110) REVERT: A 568 TRP cc_start: 0.8798 (m100) cc_final: 0.8507 (m100) REVERT: A 738 MET cc_start: 0.3870 (ppp) cc_final: 0.1310 (mmm) REVERT: A 864 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8521 (mt) REVERT: C 43 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7566 (tm-30) REVERT: C 70 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8030 (m-80) REVERT: C 76 HIS cc_start: 0.6986 (t-90) cc_final: 0.6671 (t70) REVERT: C 78 ASN cc_start: 0.7140 (m-40) cc_final: 0.6777 (m-40) REVERT: C 128 LEU cc_start: 0.8293 (mp) cc_final: 0.7888 (tt) REVERT: D 99 ARG cc_start: 0.8299 (mmp-170) cc_final: 0.7709 (mmm160) outliers start: 17 outliers final: 12 residues processed: 126 average time/residue: 0.2401 time to fit residues: 42.9306 Evaluate side-chains 124 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 149 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 116 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 114 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 102 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 = 0.4357 r_free = 0.4357 target = 0.199679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.126092 restraints weight = 12494.315| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.24 r_work: 0.3324 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10450 Z= 0.123 Angle : 0.561 10.319 14226 Z= 0.264 Chirality : 0.041 0.561 1588 Planarity : 0.004 0.052 1865 Dihedral : 5.153 58.641 1422 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 1.91 % Allowed : 15.00 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.60 (0.24), residues: 1289 helix: 1.72 (0.24), residues: 471 sheet: -0.53 (0.40), residues: 161 loop : -0.28 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 677 HIS 0.003 0.001 HIS A 908 PHE 0.010 0.001 PHE A 481 TYR 0.037 0.001 TYR B 140 ARG 0.006 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.03060 ( 411) hydrogen bonds : angle 4.55067 ( 1146) SS BOND : bond 0.00201 ( 1) SS BOND : angle 0.28816 ( 2) covalent geometry : bond 0.00299 (10447) covalent geometry : angle 0.56134 (14224) Misc. bond : bond 0.00033 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 PRO cc_start: 0.8461 (Cg_exo) cc_final: 0.8189 (Cg_endo) REVERT: A 273 GLN cc_start: 0.7498 (tm-30) cc_final: 0.7282 (tm-30) REVERT: A 373 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8770 (mm) REVERT: A 508 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7280 (mt0) REVERT: A 531 ARG cc_start: 0.7956 (mtm110) cc_final: 0.7638 (ptp-110) REVERT: A 568 TRP cc_start: 0.8765 (m100) cc_final: 0.8464 (m100) REVERT: A 677 TRP cc_start: 0.6207 (t60) cc_final: 0.5230 (t60) REVERT: A 738 MET cc_start: 0.3850 (ppp) cc_final: 0.1286 (mmm) REVERT: A 864 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8520 (mt) REVERT: C 70 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.8052 (m-80) REVERT: C 76 HIS cc_start: 0.7183 (t-90) cc_final: 0.6861 (t70) REVERT: C 78 ASN cc_start: 0.7197 (m-40) cc_final: 0.6833 (m-40) REVERT: C 128 LEU cc_start: 0.8267 (mp) cc_final: 0.7883 (tt) REVERT: D 99 ARG cc_start: 0.8278 (mmp-170) cc_final: 0.7713 (mmm160) outliers start: 21 outliers final: 14 residues processed: 126 average time/residue: 0.2821 time to fit residues: 50.8823 Evaluate side-chains 126 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 149 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 78 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 28 optimal weight: 0.0020 chunk 0 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 HIS ** D 102 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 = 0.4357 r_free = 0.4357 target = 0.199739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.126278 restraints weight = 12507.427| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.25 r_work: 0.3319 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10450 Z= 0.118 Angle : 0.559 10.318 14226 Z= 0.264 Chirality : 0.039 0.314 1588 Planarity : 0.004 0.052 1865 Dihedral : 4.868 59.105 1420 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.57 % Favored : 96.35 % Rotamer: Outliers : 1.91 % Allowed : 15.36 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.62 (0.24), residues: 1289 helix: 1.74 (0.24), residues: 471 sheet: -0.54 (0.40), residues: 161 loop : -0.26 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 677 HIS 0.003 0.001 HIS A 908 PHE 0.009 0.001 PHE A 481 TYR 0.020 0.001 TYR A 603 ARG 0.003 0.000 ARG C 23 Details of bonding type rmsd hydrogen bonds : bond 0.03001 ( 411) hydrogen bonds : angle 4.50440 ( 1146) SS BOND : bond 0.00206 ( 1) SS BOND : angle 0.34312 ( 2) covalent geometry : bond 0.00286 (10447) covalent geometry : angle 0.55952 (14224) Misc. bond : bond 0.00028 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 GLN cc_start: 0.7488 (tm-30) cc_final: 0.7265 (tm-30) REVERT: A 373 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8748 (mm) REVERT: A 508 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7261 (mt0) REVERT: A 531 ARG cc_start: 0.7966 (mtm110) cc_final: 0.7630 (ptp-110) REVERT: A 568 TRP cc_start: 0.8775 (m100) cc_final: 0.8435 (m100) REVERT: A 738 MET cc_start: 0.3846 (ppp) cc_final: 0.1328 (mmm) REVERT: A 864 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8538 (mt) REVERT: C 70 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8033 (m-80) REVERT: C 76 HIS cc_start: 0.7204 (t-90) cc_final: 0.6779 (t70) REVERT: C 78 ASN cc_start: 0.7308 (m-40) cc_final: 0.6951 (m-40) REVERT: C 128 LEU cc_start: 0.8249 (mp) cc_final: 0.7817 (tt) outliers start: 21 outliers final: 14 residues processed: 123 average time/residue: 0.2485 time to fit residues: 42.6927 Evaluate side-chains 119 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 149 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 94 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 0.0030 chunk 81 optimal weight: 10.0000 chunk 9 optimal weight: 0.4980 chunk 111 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 0.0970 chunk 0 optimal weight: 3.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** D 102 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 = 0.4363 r_free = 0.4363 target = 0.200342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.130433 restraints weight = 12462.642| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.42 r_work: 0.3307 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10450 Z= 0.100 Angle : 0.555 10.345 14226 Z= 0.261 Chirality : 0.039 0.271 1588 Planarity : 0.004 0.051 1865 Dihedral : 4.779 57.880 1420 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.59 % Rotamer: Outliers : 1.45 % Allowed : 16.27 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.66 (0.24), residues: 1289 helix: 1.76 (0.24), residues: 471 sheet: -0.50 (0.40), residues: 161 loop : -0.23 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 677 HIS 0.002 0.000 HIS A 610 PHE 0.007 0.001 PHE A 76 TYR 0.019 0.001 TYR A 603 ARG 0.007 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.02878 ( 411) hydrogen bonds : angle 4.44366 ( 1146) SS BOND : bond 0.00217 ( 1) SS BOND : angle 0.28025 ( 2) covalent geometry : bond 0.00234 (10447) covalent geometry : angle 0.55477 (14224) Misc. bond : bond 0.00020 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 GLN cc_start: 0.7508 (tm-30) cc_final: 0.7284 (tm-30) REVERT: A 373 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8713 (mm) REVERT: A 508 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7279 (mt0) REVERT: A 531 ARG cc_start: 0.8009 (mtm110) cc_final: 0.7662 (ptp-110) REVERT: A 568 TRP cc_start: 0.8800 (m100) cc_final: 0.8470 (m100) REVERT: A 738 MET cc_start: 0.3851 (ppp) cc_final: 0.1312 (mmm) REVERT: A 864 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8554 (mt) REVERT: C 43 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7628 (tm-30) REVERT: C 70 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8025 (m-80) REVERT: C 76 HIS cc_start: 0.7160 (t-90) cc_final: 0.6807 (t70) REVERT: C 78 ASN cc_start: 0.7302 (m-40) cc_final: 0.6950 (m-40) REVERT: C 128 LEU cc_start: 0.8238 (mp) cc_final: 0.7827 (tt) REVERT: D 99 ARG cc_start: 0.8236 (mmp-170) cc_final: 0.8026 (mmp-170) outliers start: 16 outliers final: 10 residues processed: 117 average time/residue: 0.2694 time to fit residues: 45.3991 Evaluate side-chains 118 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 70 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 1 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 HIS ** D 102 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 = 0.4357 r_free = 0.4357 target = 0.199440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.127676 restraints weight = 12497.300| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.34 r_work: 0.3297 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10450 Z= 0.161 Angle : 0.590 10.302 14226 Z= 0.278 Chirality : 0.041 0.313 1588 Planarity : 0.004 0.052 1865 Dihedral : 4.689 58.620 1415 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 1.64 % Allowed : 16.18 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.24), residues: 1289 helix: 1.64 (0.24), residues: 472 sheet: -0.55 (0.41), residues: 154 loop : -0.34 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 677 HIS 0.003 0.001 HIS A 291 PHE 0.010 0.001 PHE A 481 TYR 0.017 0.001 TYR A 603 ARG 0.002 0.000 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.03276 ( 411) hydrogen bonds : angle 4.58670 ( 1146) SS BOND : bond 0.00207 ( 1) SS BOND : angle 0.39805 ( 2) covalent geometry : bond 0.00395 (10447) covalent geometry : angle 0.58986 (14224) Misc. bond : bond 0.00047 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8227.20 seconds wall clock time: 148 minutes 19.94 seconds (8899.94 seconds total)