Starting phenix.real_space_refine on Wed Mar 12 04:19:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vcc_21148/03_2025/6vcc_21148.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vcc_21148/03_2025/6vcc_21148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vcc_21148/03_2025/6vcc_21148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vcc_21148/03_2025/6vcc_21148.map" model { file = "/net/cci-nas-00/data/ceres_data/6vcc_21148/03_2025/6vcc_21148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vcc_21148/03_2025/6vcc_21148.cif" } resolution = 3.6 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= 0.011 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 4896 2.51 5 N 1236 2.21 5 O 1416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7572 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "B" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "C" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "D" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "E" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "F" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "H" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "I" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "J" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "K" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "L" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Time building chain proxies: 5.02, per 1000 atoms: 0.66 Number of scatterers: 7572 At special positions: 0 Unit cell: (90, 92, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1416 8.00 N 1236 7.00 C 4896 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 1.0 seconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 15.7% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 39 through 46 removed outlier: 3.620A pdb=" N PHE A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL A 46 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.655A pdb=" N GLY A 83 " --> pdb=" O CYS A 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 46 removed outlier: 3.636A pdb=" N PHE B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 46 " --> pdb=" O ASP B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.765A pdb=" N GLY B 83 " --> pdb=" O CYS B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 46 removed outlier: 3.750A pdb=" N PHE C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL C 46 " --> pdb=" O ASP C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.609A pdb=" N GLY C 83 " --> pdb=" O CYS C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 46 removed outlier: 3.663A pdb=" N PHE D 43 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D 46 " --> pdb=" O ASP D 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 46 removed outlier: 3.757A pdb=" N PHE E 43 " --> pdb=" O THR E 39 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 46 removed outlier: 3.587A pdb=" N PHE F 43 " --> pdb=" O THR F 39 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL F 46 " --> pdb=" O ASP F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.598A pdb=" N GLY F 83 " --> pdb=" O CYS F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 48 removed outlier: 3.867A pdb=" N VAL G 46 " --> pdb=" O ASP G 42 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU G 47 " --> pdb=" O PHE G 43 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN G 48 " --> pdb=" O LYS G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.800A pdb=" N GLY G 83 " --> pdb=" O CYS G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 48 removed outlier: 3.946A pdb=" N VAL H 46 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU H 47 " --> pdb=" O PHE H 43 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN H 48 " --> pdb=" O LYS H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.529A pdb=" N GLY H 83 " --> pdb=" O CYS H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 45 Processing helix chain 'I' and resid 80 through 84 removed outlier: 3.575A pdb=" N GLY I 83 " --> pdb=" O CYS I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 48 removed outlier: 3.921A pdb=" N VAL J 46 " --> pdb=" O ASP J 42 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU J 47 " --> pdb=" O PHE J 43 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN J 48 " --> pdb=" O LYS J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 84 removed outlier: 3.527A pdb=" N GLY J 83 " --> pdb=" O CYS J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 45 Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.559A pdb=" N GLY K 83 " --> pdb=" O CYS K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 48 removed outlier: 3.895A pdb=" N VAL L 46 " --> pdb=" O ASP L 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU L 47 " --> pdb=" O PHE L 43 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN L 48 " --> pdb=" O LYS L 44 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 70 removed outlier: 5.164A pdb=" N VAL A 86 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N SER A 87 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A 17 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU A 89 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU A 28 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 14 through 18 removed outlier: 6.963A pdb=" N LEU B 28 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 14 through 16 removed outlier: 6.940A pdb=" N LEU C 28 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL D 86 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N SER D 87 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE D 17 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR D 18 " --> pdb=" O TYR D 27 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU D 28 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL E 86 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER E 87 " --> pdb=" O LYS E 15 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE E 17 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR E 18 " --> pdb=" O TYR E 27 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU E 28 " --> pdb=" O GLU F 70 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL F 86 " --> pdb=" O LYS F 58 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N SER F 87 " --> pdb=" O LYS F 15 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE F 17 " --> pdb=" O SER F 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 14 through 18 removed outlier: 3.543A pdb=" N THR G 14 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL G 29 " --> pdb=" O VAL G 16 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 87 through 89 removed outlier: 4.586A pdb=" N LYS H 30 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 17 through 18 removed outlier: 6.794A pdb=" N ILE H 17 " --> pdb=" O SER H 87 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU H 89 " --> pdb=" O ILE H 17 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL H 86 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LYS I 30 " --> pdb=" O GLU H 70 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR I 18 " --> pdb=" O TYR I 27 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR I 14 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N SER I 87 " --> pdb=" O LYS I 15 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE I 17 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU I 89 " --> pdb=" O ILE I 17 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL I 86 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS J 30 " --> pdb=" O GLU I 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 17 through 18 removed outlier: 6.863A pdb=" N ILE J 17 " --> pdb=" O SER J 87 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N LEU J 89 " --> pdb=" O ILE J 17 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL J 86 " --> pdb=" O LYS J 58 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LYS K 30 " --> pdb=" O GLU J 70 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR K 18 " --> pdb=" O TYR K 27 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR K 14 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N SER K 87 " --> pdb=" O LYS K 15 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE K 17 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU K 89 " --> pdb=" O ILE K 17 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL K 86 " --> pdb=" O LYS K 58 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS L 30 " --> pdb=" O GLU K 70 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR L 14 " --> pdb=" O ILE L 31 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 17 through 18 removed outlier: 6.658A pdb=" N ILE L 17 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU L 89 " --> pdb=" O ILE L 17 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL L 86 " --> pdb=" O LYS L 58 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2431 1.34 - 1.46: 1687 1.46 - 1.58: 3598 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 7752 Sorted by residual: bond pdb=" N LYS L 54 " pdb=" CA LYS L 54 " ideal model delta sigma weight residual 1.459 1.484 -0.024 1.23e-02 6.61e+03 3.96e+00 bond pdb=" N GLN F 48 " pdb=" CA GLN F 48 " ideal model delta sigma weight residual 1.460 1.482 -0.022 1.54e-02 4.22e+03 2.06e+00 bond pdb=" C VAL A 33 " pdb=" N PRO A 34 " ideal model delta sigma weight residual 1.326 1.345 -0.019 1.44e-02 4.82e+03 1.73e+00 bond pdb=" C VAL B 33 " pdb=" N PRO B 34 " ideal model delta sigma weight residual 1.326 1.344 -0.018 1.44e-02 4.82e+03 1.51e+00 bond pdb=" CA GLN F 48 " pdb=" CB GLN F 48 " ideal model delta sigma weight residual 1.527 1.546 -0.019 1.70e-02 3.46e+03 1.24e+00 ... (remaining 7747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 9856 1.27 - 2.53: 526 2.53 - 3.80: 91 3.80 - 5.06: 23 5.06 - 6.33: 4 Bond angle restraints: 10500 Sorted by residual: angle pdb=" C LEU F 47 " pdb=" N GLN F 48 " pdb=" CA GLN F 48 " ideal model delta sigma weight residual 122.46 127.44 -4.98 1.41e+00 5.03e-01 1.25e+01 angle pdb=" CA GLN F 48 " pdb=" CB GLN F 48 " pdb=" CG GLN F 48 " ideal model delta sigma weight residual 114.10 120.26 -6.16 2.00e+00 2.50e-01 9.50e+00 angle pdb=" N VAL B 16 " pdb=" CA VAL B 16 " pdb=" C VAL B 16 " ideal model delta sigma weight residual 106.55 110.06 -3.51 1.45e+00 4.76e-01 5.86e+00 angle pdb=" C LEU H 89 " pdb=" N VAL H 90 " pdb=" CA VAL H 90 " ideal model delta sigma weight residual 121.70 125.73 -4.03 1.80e+00 3.09e-01 5.01e+00 angle pdb=" C LEU J 89 " pdb=" N VAL J 90 " pdb=" CA VAL J 90 " ideal model delta sigma weight residual 121.70 125.70 -4.00 1.80e+00 3.09e-01 4.94e+00 ... (remaining 10495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4277 17.65 - 35.30: 347 35.30 - 52.95: 47 52.95 - 70.60: 4 70.60 - 88.24: 5 Dihedral angle restraints: 4680 sinusoidal: 1944 harmonic: 2736 Sorted by residual: dihedral pdb=" CB GLU H 24 " pdb=" CG GLU H 24 " pdb=" CD GLU H 24 " pdb=" OE1 GLU H 24 " ideal model delta sinusoidal sigma weight residual 0.00 88.24 -88.24 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU I 24 " pdb=" CG GLU I 24 " pdb=" CD GLU I 24 " pdb=" OE1 GLU I 24 " ideal model delta sinusoidal sigma weight residual 0.00 88.11 -88.11 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CA ASP D 61 " pdb=" CB ASP D 61 " pdb=" CG ASP D 61 " pdb=" OD1 ASP D 61 " ideal model delta sinusoidal sigma weight residual -30.00 -80.47 50.47 1 2.00e+01 2.50e-03 8.72e+00 ... (remaining 4677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 684 0.039 - 0.078: 292 0.078 - 0.118: 135 0.118 - 0.157: 31 0.157 - 0.196: 10 Chirality restraints: 1152 Sorted by residual: chirality pdb=" CB ILE F 38 " pdb=" CA ILE F 38 " pdb=" CG1 ILE F 38 " pdb=" CG2 ILE F 38 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" CB ILE A 38 " pdb=" CA ILE A 38 " pdb=" CG1 ILE A 38 " pdb=" CG2 ILE A 38 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CB ILE E 38 " pdb=" CA ILE E 38 " pdb=" CG1 ILE E 38 " pdb=" CG2 ILE E 38 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.23e-01 ... (remaining 1149 not shown) Planarity restraints: 1356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 33 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO C 34 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 34 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 34 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 33 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.25e+00 pdb=" N PRO H 34 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO H 34 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 34 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 77 " 0.108 9.50e-02 1.11e+02 5.00e-02 3.19e+00 pdb=" NE ARG H 77 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ARG H 77 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG H 77 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG H 77 " 0.012 2.00e-02 2.50e+03 ... (remaining 1353 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1573 2.78 - 3.31: 6085 3.31 - 3.84: 12354 3.84 - 4.37: 13207 4.37 - 4.90: 24311 Nonbonded interactions: 57530 Sorted by model distance: nonbonded pdb=" ND2 ASN D 82 " pdb=" OD1 ASP I 63 " model vdw 2.253 3.120 nonbonded pdb=" OD1 ASP E 63 " pdb=" ND2 ASN J 82 " model vdw 2.273 3.120 nonbonded pdb=" OD1 ASP D 63 " pdb=" ND2 ASN I 82 " model vdw 2.425 3.120 nonbonded pdb=" ND2 ASN E 82 " pdb=" OD1 ASP J 63 " model vdw 2.433 3.120 nonbonded pdb=" OD1 ASP B 63 " pdb=" ND2 ASN G 82 " model vdw 2.442 3.120 ... (remaining 57525 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.250 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.610 Find NCS groups from input model: 0.290 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7752 Z= 0.236 Angle : 0.664 6.330 10500 Z= 0.376 Chirality : 0.054 0.196 1152 Planarity : 0.006 0.050 1356 Dihedral : 12.504 88.244 2904 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.24), residues: 912 helix: -3.99 (0.12), residues: 72 sheet: -3.22 (0.23), residues: 360 loop : -2.61 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 88 HIS 0.004 0.002 HIS J 19 PHE 0.008 0.001 PHE E 64 TYR 0.015 0.002 TYR D 18 ARG 0.023 0.000 ARG H 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 LYS cc_start: 0.7152 (mtpp) cc_final: 0.6888 (mmtt) REVERT: B 70 GLU cc_start: 0.7086 (tt0) cc_final: 0.6733 (tt0) REVERT: C 23 GLU cc_start: 0.6398 (mt-10) cc_final: 0.6172 (mt-10) REVERT: D 15 LYS cc_start: 0.7854 (mttt) cc_final: 0.7217 (mmtt) REVERT: D 23 GLU cc_start: 0.6388 (mt-10) cc_final: 0.6174 (mt-10) REVERT: D 54 LYS cc_start: 0.7453 (mtpp) cc_final: 0.7117 (mtpt) REVERT: D 55 TYR cc_start: 0.7498 (m-80) cc_final: 0.7077 (m-80) REVERT: E 54 LYS cc_start: 0.7143 (mtpp) cc_final: 0.6724 (mtmm) REVERT: F 66 VAL cc_start: 0.8090 (m) cc_final: 0.7838 (m) REVERT: H 20 LEU cc_start: 0.8541 (mp) cc_final: 0.8293 (mt) REVERT: H 54 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7695 (mmtm) REVERT: I 72 SER cc_start: 0.7102 (m) cc_final: 0.6847 (p) REVERT: J 60 MET cc_start: 0.8315 (tpp) cc_final: 0.8097 (tpp) REVERT: K 49 ARG cc_start: 0.6228 (mmm160) cc_final: 0.5993 (mmp80) REVERT: K 69 GLU cc_start: 0.6371 (pt0) cc_final: 0.5993 (pt0) REVERT: K 74 ASP cc_start: 0.6733 (m-30) cc_final: 0.6384 (p0) REVERT: L 34 PRO cc_start: 0.6822 (Cg_endo) cc_final: 0.6132 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2483 time to fit residues: 71.2483 Evaluate side-chains 184 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 GLN G 82 ASN J 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.216327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.182022 restraints weight = 7473.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.185287 restraints weight = 6103.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.188172 restraints weight = 5230.446| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 7752 Z= 0.360 Angle : 0.678 9.569 10500 Z= 0.330 Chirality : 0.051 0.156 1152 Planarity : 0.006 0.053 1356 Dihedral : 4.537 13.352 1008 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.81 % Allowed : 15.00 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.25), residues: 912 helix: -1.37 (0.42), residues: 72 sheet: -3.10 (0.24), residues: 360 loop : -2.38 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 88 HIS 0.007 0.003 HIS B 19 PHE 0.019 0.002 PHE G 57 TYR 0.017 0.002 TYR A 27 ARG 0.005 0.001 ARG L 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 LYS cc_start: 0.8118 (tttt) cc_final: 0.7791 (tttp) REVERT: D 54 LYS cc_start: 0.7524 (mtpp) cc_final: 0.7223 (mtpt) REVERT: D 70 GLU cc_start: 0.5765 (tt0) cc_final: 0.5372 (tt0) REVERT: H 54 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7820 (mmtm) REVERT: K 54 LYS cc_start: 0.8177 (mmmt) cc_final: 0.7863 (mmmt) outliers start: 32 outliers final: 19 residues processed: 223 average time/residue: 0.2614 time to fit residues: 73.2903 Evaluate side-chains 205 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.210435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.177928 restraints weight = 7538.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.181713 restraints weight = 5963.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.184575 restraints weight = 4993.997| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7752 Z= 0.353 Angle : 0.639 9.629 10500 Z= 0.311 Chirality : 0.051 0.146 1152 Planarity : 0.005 0.052 1356 Dihedral : 4.684 15.992 1008 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.17 % Allowed : 18.10 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.26), residues: 912 helix: -0.16 (0.55), residues: 84 sheet: -2.85 (0.24), residues: 360 loop : -2.17 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 88 HIS 0.006 0.002 HIS A 19 PHE 0.016 0.002 PHE G 57 TYR 0.014 0.002 TYR G 55 ARG 0.003 0.000 ARG L 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: B 58 LYS cc_start: 0.8112 (tttt) cc_final: 0.7837 (tttp) REVERT: D 15 LYS cc_start: 0.8288 (mttt) cc_final: 0.7840 (ptmt) REVERT: D 54 LYS cc_start: 0.7704 (mtpp) cc_final: 0.7382 (mtpt) REVERT: I 30 LYS cc_start: 0.7861 (mmtp) cc_final: 0.7659 (mttt) REVERT: J 17 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8413 (mt) REVERT: J 60 MET cc_start: 0.8412 (tpp) cc_final: 0.8203 (tpp) outliers start: 35 outliers final: 27 residues processed: 220 average time/residue: 0.2375 time to fit residues: 66.3102 Evaluate side-chains 216 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 37 optimal weight: 30.0000 chunk 46 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 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 = 0.4279 r_free = 0.4279 target = 0.208460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.174325 restraints weight = 7600.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.178499 restraints weight = 5835.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.181552 restraints weight = 4810.232| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7752 Z= 0.323 Angle : 0.624 9.817 10500 Z= 0.303 Chirality : 0.051 0.196 1152 Planarity : 0.005 0.049 1356 Dihedral : 4.590 15.102 1008 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.40 % Allowed : 18.93 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.27), residues: 912 helix: 0.44 (0.61), residues: 84 sheet: -2.51 (0.25), residues: 348 loop : -2.09 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 88 HIS 0.004 0.002 HIS F 19 PHE 0.021 0.002 PHE L 64 TYR 0.013 0.002 TYR B 27 ARG 0.006 0.000 ARG K 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8183 (mttt) cc_final: 0.7698 (mttt) REVERT: D 54 LYS cc_start: 0.7885 (mtpp) cc_final: 0.7560 (mtpt) REVERT: E 54 LYS cc_start: 0.7733 (mmmt) cc_final: 0.6967 (mptt) REVERT: F 27 TYR cc_start: 0.7223 (m-80) cc_final: 0.6300 (m-80) REVERT: F 60 MET cc_start: 0.7765 (tpp) cc_final: 0.6582 (tmm) REVERT: G 71 ILE cc_start: 0.8449 (mm) cc_final: 0.8247 (mm) REVERT: J 17 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8375 (mt) REVERT: K 54 LYS cc_start: 0.8397 (mmmt) cc_final: 0.8144 (mmmt) REVERT: K 74 ASP cc_start: 0.5774 (p0) cc_final: 0.5525 (p0) REVERT: L 81 PHE cc_start: 0.7351 (t80) cc_final: 0.7142 (t80) outliers start: 37 outliers final: 28 residues processed: 212 average time/residue: 0.2428 time to fit residues: 65.2310 Evaluate side-chains 213 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 36 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 59 optimal weight: 0.0570 chunk 53 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 overall best weight: 3.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.208553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.177516 restraints weight = 7444.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.181253 restraints weight = 5783.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.184029 restraints weight = 4800.407| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7752 Z= 0.274 Angle : 0.596 9.590 10500 Z= 0.289 Chirality : 0.050 0.157 1152 Planarity : 0.005 0.049 1356 Dihedral : 4.483 13.999 1008 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.64 % Allowed : 20.00 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.28), residues: 912 helix: 0.68 (0.63), residues: 84 sheet: -2.29 (0.26), residues: 348 loop : -1.96 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 88 HIS 0.004 0.002 HIS F 19 PHE 0.022 0.002 PHE L 64 TYR 0.012 0.002 TYR A 27 ARG 0.006 0.000 ARG K 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8149 (mttt) cc_final: 0.7654 (mttt) REVERT: D 54 LYS cc_start: 0.7886 (mtpp) cc_final: 0.7554 (mtpt) REVERT: E 54 LYS cc_start: 0.7690 (mmmt) cc_final: 0.6975 (mptt) REVERT: E 69 GLU cc_start: 0.7579 (pt0) cc_final: 0.7298 (pt0) REVERT: F 60 MET cc_start: 0.7801 (tpp) cc_final: 0.6491 (tmm) REVERT: G 71 ILE cc_start: 0.8514 (mm) cc_final: 0.8303 (mm) REVERT: I 30 LYS cc_start: 0.7787 (mttt) cc_final: 0.7413 (ttmt) REVERT: J 17 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8435 (mt) REVERT: J 24 GLU cc_start: 0.5373 (mm-30) cc_final: 0.4674 (mm-30) REVERT: L 20 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7507 (mp) REVERT: L 81 PHE cc_start: 0.7263 (t80) cc_final: 0.7058 (t80) outliers start: 39 outliers final: 29 residues processed: 216 average time/residue: 0.2393 time to fit residues: 65.9084 Evaluate side-chains 217 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 17 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 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 = 0.4294 r_free = 0.4294 target = 0.209569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.175801 restraints weight = 7483.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.180523 restraints weight = 5455.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.184013 restraints weight = 4347.948| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7752 Z= 0.261 Angle : 0.592 9.437 10500 Z= 0.286 Chirality : 0.050 0.231 1152 Planarity : 0.004 0.050 1356 Dihedral : 4.401 15.642 1008 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.24 % Allowed : 20.24 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.28), residues: 912 helix: 0.89 (0.63), residues: 84 sheet: -2.03 (0.25), residues: 384 loop : -1.99 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 88 HIS 0.003 0.002 HIS F 19 PHE 0.012 0.002 PHE I 64 TYR 0.012 0.002 TYR B 27 ARG 0.003 0.000 ARG F 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8126 (mttt) cc_final: 0.7613 (mttt) REVERT: E 54 LYS cc_start: 0.7725 (mmmt) cc_final: 0.7430 (mmmt) REVERT: E 69 GLU cc_start: 0.7630 (pt0) cc_final: 0.7346 (pt0) REVERT: F 60 MET cc_start: 0.7772 (tpp) cc_final: 0.6443 (tmm) REVERT: G 71 ILE cc_start: 0.8456 (mm) cc_final: 0.8249 (mm) REVERT: J 17 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8444 (mt) REVERT: J 24 GLU cc_start: 0.5485 (mm-30) cc_final: 0.4755 (mm-30) REVERT: J 64 PHE cc_start: 0.8199 (m-80) cc_final: 0.7959 (m-80) REVERT: K 54 LYS cc_start: 0.8355 (mmmt) cc_final: 0.8036 (mmmt) REVERT: L 20 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7515 (mp) REVERT: L 81 PHE cc_start: 0.7442 (t80) cc_final: 0.7156 (t80) outliers start: 44 outliers final: 35 residues processed: 215 average time/residue: 0.2289 time to fit residues: 62.5256 Evaluate side-chains 226 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 20 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.188748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.153658 restraints weight = 7543.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.157123 restraints weight = 5899.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.159742 restraints weight = 4903.010| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7752 Z= 0.289 Angle : 0.609 9.549 10500 Z= 0.295 Chirality : 0.050 0.141 1152 Planarity : 0.005 0.053 1356 Dihedral : 4.459 17.719 1008 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 5.60 % Allowed : 19.88 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.28), residues: 912 helix: 0.90 (0.63), residues: 84 sheet: -1.99 (0.26), residues: 372 loop : -1.96 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 88 HIS 0.004 0.002 HIS F 19 PHE 0.013 0.002 PHE I 64 TYR 0.012 0.002 TYR A 27 ARG 0.008 0.000 ARG D 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: C 40 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7062 (tp) REVERT: D 15 LYS cc_start: 0.8179 (mttt) cc_final: 0.7637 (mttt) REVERT: E 54 LYS cc_start: 0.7884 (mmmt) cc_final: 0.7455 (mmmt) REVERT: E 69 GLU cc_start: 0.7655 (pt0) cc_final: 0.7280 (pt0) REVERT: F 60 MET cc_start: 0.7775 (tpp) cc_final: 0.6561 (tmm) REVERT: J 17 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8422 (mt) REVERT: J 24 GLU cc_start: 0.5536 (mm-30) cc_final: 0.4759 (mm-30) REVERT: J 64 PHE cc_start: 0.8282 (m-80) cc_final: 0.8051 (m-80) REVERT: K 54 LYS cc_start: 0.8383 (mmmt) cc_final: 0.8064 (mmmt) REVERT: L 20 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7584 (mp) outliers start: 47 outliers final: 38 residues processed: 218 average time/residue: 0.2618 time to fit residues: 72.9738 Evaluate side-chains 229 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 62 GLN Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 65 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 44 optimal weight: 0.0470 overall best weight: 1.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.190815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.155338 restraints weight = 7582.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.158973 restraints weight = 5846.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.161449 restraints weight = 4834.074| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7752 Z= 0.176 Angle : 0.565 8.764 10500 Z= 0.273 Chirality : 0.049 0.137 1152 Planarity : 0.004 0.050 1356 Dihedral : 4.173 13.695 1008 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.93 % Allowed : 22.14 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.29), residues: 912 helix: 1.10 (0.62), residues: 84 sheet: -1.77 (0.26), residues: 384 loop : -1.77 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 88 HIS 0.002 0.001 HIS I 19 PHE 0.018 0.001 PHE L 81 TYR 0.010 0.001 TYR B 27 ARG 0.007 0.000 ARG D 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8084 (mttt) cc_final: 0.7561 (mttt) REVERT: D 46 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.7809 (p) REVERT: E 54 LYS cc_start: 0.7885 (mmmt) cc_final: 0.7408 (mmmt) REVERT: E 69 GLU cc_start: 0.7667 (pt0) cc_final: 0.7335 (pt0) REVERT: F 60 MET cc_start: 0.7788 (tpp) cc_final: 0.6546 (tmm) REVERT: I 60 MET cc_start: 0.8370 (tpp) cc_final: 0.8089 (tpp) REVERT: J 17 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8438 (mt) REVERT: J 24 GLU cc_start: 0.5739 (mm-30) cc_final: 0.4947 (mm-30) REVERT: J 64 PHE cc_start: 0.8205 (m-80) cc_final: 0.7920 (m-80) REVERT: K 54 LYS cc_start: 0.8288 (mmmt) cc_final: 0.7936 (mmmt) outliers start: 33 outliers final: 30 residues processed: 215 average time/residue: 0.2618 time to fit residues: 70.3687 Evaluate side-chains 222 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 0.0030 chunk 64 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN J 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.193614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.157959 restraints weight = 7648.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.162792 restraints weight = 6829.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.164791 restraints weight = 5024.742| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7752 Z= 0.155 Angle : 0.555 8.427 10500 Z= 0.267 Chirality : 0.049 0.136 1152 Planarity : 0.004 0.052 1356 Dihedral : 4.007 14.172 1008 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.57 % Allowed : 23.21 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.29), residues: 912 helix: 1.35 (0.62), residues: 84 sheet: -1.67 (0.26), residues: 384 loop : -1.64 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 88 HIS 0.002 0.001 HIS B 19 PHE 0.015 0.001 PHE L 81 TYR 0.009 0.001 TYR A 27 ARG 0.007 0.000 ARG D 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: C 60 MET cc_start: 0.7834 (tpp) cc_final: 0.6849 (ttm) REVERT: D 15 LYS cc_start: 0.8048 (mttt) cc_final: 0.7529 (mttt) REVERT: D 46 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.7780 (p) REVERT: E 54 LYS cc_start: 0.7893 (mmmt) cc_final: 0.7271 (mmmt) REVERT: E 69 GLU cc_start: 0.7658 (pt0) cc_final: 0.7326 (pt0) REVERT: F 60 MET cc_start: 0.7705 (tpp) cc_final: 0.6502 (tmm) REVERT: G 77 ARG cc_start: 0.6799 (ptm160) cc_final: 0.6466 (ptm160) REVERT: I 60 MET cc_start: 0.8322 (tpp) cc_final: 0.8105 (tpp) REVERT: J 17 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8431 (mt) REVERT: J 24 GLU cc_start: 0.5646 (mm-30) cc_final: 0.4746 (mm-30) REVERT: K 54 LYS cc_start: 0.8230 (mmmt) cc_final: 0.7876 (mmmt) outliers start: 30 outliers final: 25 residues processed: 211 average time/residue: 0.2358 time to fit residues: 63.6419 Evaluate side-chains 215 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 64 optimal weight: 0.0070 chunk 16 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 0.0770 chunk 26 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.194508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.160718 restraints weight = 7558.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.163684 restraints weight = 5884.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.166251 restraints weight = 4930.834| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7752 Z= 0.187 Angle : 0.574 9.340 10500 Z= 0.274 Chirality : 0.049 0.140 1152 Planarity : 0.004 0.054 1356 Dihedral : 4.035 15.281 1008 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.69 % Allowed : 23.10 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.29), residues: 912 helix: 1.47 (0.62), residues: 84 sheet: -1.63 (0.26), residues: 384 loop : -1.57 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 88 HIS 0.002 0.001 HIS K 19 PHE 0.024 0.002 PHE J 64 TYR 0.010 0.001 TYR A 27 ARG 0.008 0.000 ARG D 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: C 40 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7037 (tp) REVERT: C 60 MET cc_start: 0.7830 (tpp) cc_final: 0.6864 (ttm) REVERT: D 15 LYS cc_start: 0.8034 (mttt) cc_final: 0.7533 (mttt) REVERT: D 46 VAL cc_start: 0.8220 (m) cc_final: 0.7770 (p) REVERT: E 54 LYS cc_start: 0.7813 (mmmt) cc_final: 0.7194 (mmmt) REVERT: E 69 GLU cc_start: 0.7661 (pt0) cc_final: 0.7343 (pt0) REVERT: F 60 MET cc_start: 0.7747 (tpp) cc_final: 0.6536 (tmm) REVERT: I 60 MET cc_start: 0.8320 (tpp) cc_final: 0.8117 (tpp) REVERT: J 17 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8429 (mt) REVERT: J 24 GLU cc_start: 0.5754 (mm-30) cc_final: 0.4923 (mm-30) REVERT: K 54 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7823 (mmmt) outliers start: 31 outliers final: 28 residues processed: 208 average time/residue: 0.2569 time to fit residues: 68.9364 Evaluate side-chains 218 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.0370 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** 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 = 0.4123 r_free = 0.4123 target = 0.190797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.154653 restraints weight = 7465.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.158494 restraints weight = 5600.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.161450 restraints weight = 4549.821| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7752 Z= 0.295 Angle : 0.633 10.909 10500 Z= 0.302 Chirality : 0.050 0.141 1152 Planarity : 0.005 0.057 1356 Dihedral : 4.398 16.433 1008 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.17 % Allowed : 22.98 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.29), residues: 912 helix: 1.40 (0.63), residues: 84 sheet: -1.74 (0.26), residues: 384 loop : -1.56 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 88 HIS 0.004 0.002 HIS F 19 PHE 0.018 0.002 PHE L 81 TYR 0.014 0.002 TYR B 27 ARG 0.008 0.001 ARG D 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2638.50 seconds wall clock time: 46 minutes 51.91 seconds (2811.91 seconds total)