Starting phenix.real_space_refine on Mon Dec 30 01:42:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hr1_34956/12_2024/8hr1_34956.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hr1_34956/12_2024/8hr1_34956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hr1_34956/12_2024/8hr1_34956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hr1_34956/12_2024/8hr1_34956.map" model { file = "/net/cci-nas-00/data/ceres_data/8hr1_34956/12_2024/8hr1_34956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hr1_34956/12_2024/8hr1_34956.cif" } resolution = 3.02 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= 0.002 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 294 5.49 5 S 11 5.16 5 C 6695 2.51 5 N 2275 2.21 5 O 2835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12110 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 707 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 707 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "S" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'CIS': 1, 'TRANS': 12} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 7.34, per 1000 atoms: 0.61 Number of scatterers: 12110 At special positions: 0 Unit cell: (119.214, 92.364, 117.066, 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 11 16.00 P 294 15.00 O 2835 8.00 N 2275 7.00 C 6695 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: 3.28 Conformation dependent library (CDL) restraints added in 1.1 seconds 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 70.2% alpha, 2.6% beta 136 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 7.55 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 4.401A pdb=" N ARG A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.761A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 removed outlier: 4.044A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.772A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.793A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.562A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.372A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.819A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.554A pdb=" N GLU D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.564A pdb=" N ALA D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.606A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.553A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.940A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.625A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 48 through 51 removed outlier: 3.803A pdb=" N TYR F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 48 through 51' Processing helix chain 'F' and resid 54 through 76 removed outlier: 3.631A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.705A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.384A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU G 63 " --> pdb=" O THR G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.562A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.553A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA H 81 " --> pdb=" O ALA H 77 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.565A pdb=" N ALA H 97 " --> pdb=" O GLU H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.606A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.904A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.259A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.314A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.057A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.382A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 354 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 326 hydrogen bonds 584 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 4.94 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2260 1.33 - 1.45: 4320 1.45 - 1.57: 5738 1.57 - 1.69: 586 1.69 - 1.80: 21 Bond restraints: 12925 Sorted by residual: bond pdb=" C LEU H 101 " pdb=" N LEU H 102 " ideal model delta sigma weight residual 1.331 1.294 0.037 1.63e-02 3.76e+03 5.28e+00 bond pdb=" CB ARG B 92 " pdb=" CG ARG B 92 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.90e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.483 -0.061 3.00e-02 1.11e+03 4.10e+00 bond pdb=" CG1 ILE F 50 " pdb=" CD1 ILE F 50 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.91e+00 bond pdb=" C ILE A 119 " pdb=" N MET A 120 " ideal model delta sigma weight residual 1.329 1.273 0.055 3.03e-02 1.09e+03 3.33e+00 ... (remaining 12920 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 17648 1.63 - 3.26: 961 3.26 - 4.89: 76 4.89 - 6.51: 21 6.51 - 8.14: 9 Bond angle restraints: 18715 Sorted by residual: angle pdb=" C LEU H 101 " pdb=" N LEU H 102 " pdb=" CA LEU H 102 " ideal model delta sigma weight residual 121.61 116.53 5.08 1.39e+00 5.18e-01 1.33e+01 angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sigma weight residual 120.20 125.21 -5.01 1.50e+00 4.44e-01 1.12e+01 angle pdb=" C PHE E 104 " pdb=" N GLU E 105 " pdb=" CA GLU E 105 " ideal model delta sigma weight residual 121.14 115.49 5.65 1.75e+00 3.27e-01 1.04e+01 angle pdb=" C PHE H 70 " pdb=" N GLU H 71 " pdb=" CA GLU H 71 " ideal model delta sigma weight residual 121.94 115.91 6.03 2.00e+00 2.50e-01 9.09e+00 angle pdb=" C PHE D 70 " pdb=" N GLU D 71 " pdb=" CA GLU D 71 " ideal model delta sigma weight residual 121.94 115.96 5.98 2.00e+00 2.50e-01 8.94e+00 ... (remaining 18710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.36: 5757 35.36 - 70.72: 1232 70.72 - 106.08: 15 106.08 - 141.44: 2 141.44 - 176.80: 1 Dihedral angle restraints: 7007 sinusoidal: 4791 harmonic: 2216 Sorted by residual: dihedral pdb=" CA ALA A 127 " pdb=" C ALA A 127 " pdb=" N ARG A 128 " pdb=" CA ARG A 128 " ideal model delta harmonic sigma weight residual 180.00 155.70 24.30 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ALA A 114 " pdb=" C ALA A 114 " pdb=" N LYS A 115 " pdb=" CA LYS A 115 " ideal model delta harmonic sigma weight residual 180.00 158.56 21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA ARG S 169 " pdb=" C ARG S 169 " pdb=" N GLU S 170 " pdb=" CA GLU S 170 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 7004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1199 0.038 - 0.076: 761 0.076 - 0.114: 120 0.114 - 0.152: 37 0.152 - 0.191: 14 Chirality restraints: 2131 Sorted by residual: chirality pdb=" CB ILE H 54 " pdb=" CA ILE H 54 " pdb=" CG1 ILE H 54 " pdb=" CG2 ILE H 54 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.08e-01 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CA ILE G 79 " pdb=" N ILE G 79 " pdb=" C ILE G 79 " pdb=" CB ILE G 79 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.30e-01 ... (remaining 2128 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO A 66 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO G 80 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 69 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C ILE H 69 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE H 69 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE H 70 " 0.011 2.00e-02 2.50e+03 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2666 2.78 - 3.31: 10387 3.31 - 3.84: 24457 3.84 - 4.37: 28931 4.37 - 4.90: 40663 Nonbonded interactions: 107104 Sorted by model distance: nonbonded pdb=" OE1 GLN A 68 " pdb=" NH1 ARG A 72 " model vdw 2.255 3.120 nonbonded pdb=" OH TYR G 57 " pdb=" OE2 GLU G 61 " model vdw 2.305 3.040 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.310 3.040 nonbonded pdb=" OG SER C 40 " pdb=" O ARG C 42 " model vdw 2.340 3.040 nonbonded pdb=" N4 DC I 40 " pdb=" O6 DG J -40 " model vdw 2.340 3.120 ... (remaining 107099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 13 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 0.900 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 35.630 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.010 0.077 12925 Z= 0.555 Angle : 0.803 8.143 18715 Z= 0.470 Chirality : 0.047 0.191 2131 Planarity : 0.005 0.050 1346 Dihedral : 26.086 176.798 5577 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.16 % Allowed : 3.60 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: -5.09 (0.20), residues: 747 helix: -3.62 (0.12), residues: 530 sheet: None (None), residues: 0 loop : -2.00 (0.36), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.007 TRP S 164 HIS 0.014 0.002 HIS C 82 PHE 0.031 0.004 PHE E 104 TYR 0.013 0.002 TYR F 88 ARG 0.009 0.001 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.968 Fit side-chains REVERT: A 68 GLN cc_start: 0.8635 (tm130) cc_final: 0.8354 (tm-30) REVERT: A 79 LYS cc_start: 0.7632 (tttp) cc_final: 0.7367 (tttt) REVERT: A 125 GLN cc_start: 0.8576 (mt0) cc_final: 0.8318 (mt0) REVERT: B 59 LYS cc_start: 0.8150 (tptt) cc_final: 0.7779 (tptp) REVERT: B 63 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7864 (mt-10) REVERT: B 74 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8290 (mt-10) REVERT: B 88 TYR cc_start: 0.8163 (m-10) cc_final: 0.7671 (m-80) REVERT: B 91 LYS cc_start: 0.8526 (ttmt) cc_final: 0.7920 (ttpt) REVERT: B 95 ARG cc_start: 0.7903 (mtt90) cc_final: 0.7572 (mtt-85) REVERT: C 36 LYS cc_start: 0.8576 (ptpt) cc_final: 0.8192 (pptt) REVERT: C 41 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8133 (tt0) REVERT: C 56 GLU cc_start: 0.8050 (tt0) cc_final: 0.7738 (tt0) REVERT: C 95 LYS cc_start: 0.8930 (ttmp) cc_final: 0.8670 (tttm) REVERT: C 107 VAL cc_start: 0.8707 (t) cc_final: 0.8098 (m) REVERT: D 36 SER cc_start: 0.8174 (t) cc_final: 0.7921 (t) REVERT: D 46 LYS cc_start: 0.8764 (mmpt) cc_final: 0.8458 (mmmt) REVERT: D 57 LYS cc_start: 0.8282 (mmtp) cc_final: 0.8001 (mmtt) REVERT: D 71 GLU cc_start: 0.8139 (pm20) cc_final: 0.7915 (pm20) REVERT: D 82 HIS cc_start: 0.8301 (m-70) cc_final: 0.7819 (m-70) REVERT: D 105 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7696 (mm-30) REVERT: D 108 LYS cc_start: 0.8481 (mttt) cc_final: 0.7820 (mtpp) REVERT: E 41 TYR cc_start: 0.6964 (m-80) cc_final: 0.6592 (m-10) REVERT: E 64 LYS cc_start: 0.7668 (mtmt) cc_final: 0.7280 (mttp) REVERT: E 79 LYS cc_start: 0.7849 (tttp) cc_final: 0.7279 (ttpt) REVERT: E 129 ARG cc_start: 0.8467 (tmt-80) cc_final: 0.7955 (tpt90) REVERT: F 25 ASN cc_start: 0.8932 (OUTLIER) cc_final: 0.8380 (t0) REVERT: F 27 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8404 (mm-40) REVERT: F 44 LYS cc_start: 0.8357 (ttpt) cc_final: 0.8127 (ttmt) REVERT: F 63 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7927 (mt-10) REVERT: F 74 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8421 (mt-10) REVERT: F 91 LYS cc_start: 0.8512 (ttmt) cc_final: 0.7925 (ttpt) REVERT: G 64 GLU cc_start: 0.8468 (tp30) cc_final: 0.8261 (tp30) REVERT: G 95 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8323 (ttmm) REVERT: G 107 VAL cc_start: 0.8493 (t) cc_final: 0.8151 (m) REVERT: H 40 TYR cc_start: 0.8462 (m-80) cc_final: 0.8160 (m-80) REVERT: H 68 ASP cc_start: 0.8848 (t70) cc_final: 0.8416 (t0) REVERT: H 71 GLU cc_start: 0.7967 (pm20) cc_final: 0.7303 (mp0) REVERT: H 76 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7888 (tp30) REVERT: H 85 LYS cc_start: 0.8493 (mptm) cc_final: 0.8222 (mmtt) REVERT: H 93 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7897 (mm-30) REVERT: H 108 LYS cc_start: 0.8757 (mttt) cc_final: 0.8446 (mmtp) outliers start: 1 outliers final: 0 residues processed: 230 average time/residue: 0.4638 time to fit residues: 131.0577 Evaluate side-chains 151 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 25 ASN D 84 ASN E 68 GLN E 125 GLN G 94 ASN H 84 ASN H 95 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12925 Z= 0.224 Angle : 0.627 9.940 18715 Z= 0.377 Chirality : 0.037 0.155 2131 Planarity : 0.005 0.039 1346 Dihedral : 30.383 169.725 4063 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.19 % Allowed : 7.82 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.27), residues: 747 helix: -0.78 (0.19), residues: 545 sheet: None (None), residues: 0 loop : -1.79 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.006 TRP S 164 HIS 0.006 0.001 HIS C 31 PHE 0.014 0.002 PHE G 25 TYR 0.012 0.001 TYR D 40 ARG 0.005 0.001 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.972 Fit side-chains REVERT: A 79 LYS cc_start: 0.7828 (tttp) cc_final: 0.7534 (tttt) REVERT: A 93 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: A 94 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8041 (mm-30) REVERT: A 125 GLN cc_start: 0.8560 (mt0) cc_final: 0.8315 (mt0) REVERT: B 35 ARG cc_start: 0.8314 (mtp85) cc_final: 0.8035 (mtp85) REVERT: B 63 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7851 (mt-10) REVERT: B 95 ARG cc_start: 0.7897 (mtt90) cc_final: 0.7463 (mtp85) REVERT: C 35 ARG cc_start: 0.8266 (mtm-85) cc_final: 0.7912 (mtm-85) REVERT: C 41 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8088 (tt0) REVERT: C 95 LYS cc_start: 0.8885 (ttmp) cc_final: 0.8522 (tttp) REVERT: D 46 LYS cc_start: 0.8431 (mmpt) cc_final: 0.8153 (mmmt) REVERT: D 57 LYS cc_start: 0.7652 (mmtp) cc_final: 0.7428 (mmtt) REVERT: D 63 ASN cc_start: 0.8150 (t0) cc_final: 0.7794 (m-40) REVERT: D 82 HIS cc_start: 0.8252 (m-70) cc_final: 0.7953 (m-70) REVERT: D 86 ARG cc_start: 0.7995 (mtp85) cc_final: 0.7639 (mmt90) REVERT: D 105 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7730 (mm-30) REVERT: D 108 LYS cc_start: 0.8716 (mttt) cc_final: 0.8172 (mtpp) REVERT: D 113 GLU cc_start: 0.8432 (tp30) cc_final: 0.8177 (tp30) REVERT: E 41 TYR cc_start: 0.7244 (m-80) cc_final: 0.6948 (m-10) REVERT: E 73 GLU cc_start: 0.8288 (pt0) cc_final: 0.7600 (pt0) REVERT: E 76 GLN cc_start: 0.8049 (tt0) cc_final: 0.7743 (tt0) REVERT: E 79 LYS cc_start: 0.7364 (tttp) cc_final: 0.6743 (ttpt) REVERT: E 129 ARG cc_start: 0.8526 (tmt-80) cc_final: 0.8028 (tpt90) REVERT: F 25 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8877 (m-40) REVERT: F 35 ARG cc_start: 0.7892 (mtp85) cc_final: 0.7427 (mtp85) REVERT: F 78 ARG cc_start: 0.8573 (mtm-85) cc_final: 0.8289 (mtm110) REVERT: F 91 LYS cc_start: 0.8675 (ttmt) cc_final: 0.8171 (ttpt) REVERT: G 13 LYS cc_start: 0.5682 (OUTLIER) cc_final: 0.5303 (pttm) REVERT: G 41 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8167 (mt-10) REVERT: G 79 ILE cc_start: 0.8137 (tp) cc_final: 0.7853 (pt) REVERT: H 68 ASP cc_start: 0.8677 (t70) cc_final: 0.8383 (t0) REVERT: H 85 LYS cc_start: 0.8619 (mptm) cc_final: 0.8287 (mmtt) REVERT: H 108 LYS cc_start: 0.8926 (mttt) cc_final: 0.8697 (mttm) REVERT: S 172 LYS cc_start: 0.8228 (mmmt) cc_final: 0.7913 (mmmm) outliers start: 14 outliers final: 5 residues processed: 193 average time/residue: 0.3583 time to fit residues: 89.2942 Evaluate side-chains 156 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain S residue 168 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN E 68 GLN E 93 GLN F 25 ASN F 93 GLN G 68 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 12925 Z= 0.398 Angle : 0.665 7.105 18715 Z= 0.391 Chirality : 0.041 0.158 2131 Planarity : 0.005 0.048 1346 Dihedral : 30.805 159.906 4063 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.60 % Allowed : 13.30 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.29), residues: 747 helix: 0.36 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -1.67 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.006 TRP S 164 HIS 0.011 0.002 HIS C 31 PHE 0.030 0.003 PHE G 25 TYR 0.014 0.002 TYR D 40 ARG 0.006 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.794 Fit side-chains REVERT: A 73 GLU cc_start: 0.8056 (tt0) cc_final: 0.7628 (tt0) REVERT: A 79 LYS cc_start: 0.7824 (tttp) cc_final: 0.7544 (tttt) REVERT: A 93 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: A 94 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7949 (mm-30) REVERT: A 105 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7642 (mt-10) REVERT: B 25 ASN cc_start: 0.8084 (m-40) cc_final: 0.7571 (m110) REVERT: B 63 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7901 (mt-10) REVERT: C 41 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8105 (tt0) REVERT: C 95 LYS cc_start: 0.8912 (ttmp) cc_final: 0.8645 (tttt) REVERT: D 57 LYS cc_start: 0.7832 (mmtp) cc_final: 0.7549 (mmtt) REVERT: D 82 HIS cc_start: 0.8066 (m-70) cc_final: 0.7687 (m-70) REVERT: D 86 ARG cc_start: 0.8140 (mtp85) cc_final: 0.7762 (mmt90) REVERT: D 105 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7683 (mm-30) REVERT: D 108 LYS cc_start: 0.8747 (mttt) cc_final: 0.8112 (mtpt) REVERT: D 113 GLU cc_start: 0.8909 (tp30) cc_final: 0.8632 (tp30) REVERT: E 41 TYR cc_start: 0.7494 (m-80) cc_final: 0.7241 (m-10) REVERT: E 64 LYS cc_start: 0.7768 (mttt) cc_final: 0.7442 (mttt) REVERT: E 79 LYS cc_start: 0.7368 (tttp) cc_final: 0.7121 (tttm) REVERT: F 35 ARG cc_start: 0.7880 (mtp85) cc_final: 0.7547 (mtp85) REVERT: F 91 LYS cc_start: 0.8695 (ttmt) cc_final: 0.8303 (ttpt) REVERT: G 61 GLU cc_start: 0.8021 (tt0) cc_final: 0.7736 (tp30) REVERT: G 64 GLU cc_start: 0.8359 (tp30) cc_final: 0.7937 (tm-30) REVERT: H 68 ASP cc_start: 0.8653 (t70) cc_final: 0.8188 (t0) REVERT: H 85 LYS cc_start: 0.8698 (mptm) cc_final: 0.8135 (mmtp) outliers start: 23 outliers final: 11 residues processed: 160 average time/residue: 0.3344 time to fit residues: 71.4052 Evaluate side-chains 153 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.0670 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 125 GLN C 38 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12925 Z= 0.185 Angle : 0.555 6.925 18715 Z= 0.338 Chirality : 0.034 0.172 2131 Planarity : 0.004 0.041 1346 Dihedral : 30.441 158.518 4061 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.50 % Allowed : 13.30 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.75 (0.30), residues: 747 helix: 1.21 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.40 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP S 164 HIS 0.003 0.001 HIS D 109 PHE 0.011 0.001 PHE E 67 TYR 0.012 0.001 TYR D 40 ARG 0.004 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.977 Fit side-chains REVERT: A 59 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7076 (pm20) REVERT: A 73 GLU cc_start: 0.7953 (tt0) cc_final: 0.7726 (tt0) REVERT: A 79 LYS cc_start: 0.7871 (tttp) cc_final: 0.7666 (tttt) REVERT: A 105 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7589 (mt-10) REVERT: A 115 LYS cc_start: 0.9035 (mttt) cc_final: 0.8769 (mmtt) REVERT: B 25 ASN cc_start: 0.7892 (m-40) cc_final: 0.7261 (m110) REVERT: B 59 LYS cc_start: 0.8087 (tttt) cc_final: 0.7865 (tttp) REVERT: B 63 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7797 (mt-10) REVERT: B 88 TYR cc_start: 0.8026 (m-10) cc_final: 0.7600 (m-80) REVERT: C 95 LYS cc_start: 0.8912 (ttmp) cc_final: 0.8632 (tttt) REVERT: D 46 LYS cc_start: 0.8511 (mmpt) cc_final: 0.8194 (mmmt) REVERT: D 82 HIS cc_start: 0.8029 (m-70) cc_final: 0.7531 (m-70) REVERT: D 86 ARG cc_start: 0.8102 (mtp85) cc_final: 0.7561 (mmt90) REVERT: D 93 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7471 (mp0) REVERT: D 105 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7735 (mm-30) REVERT: D 108 LYS cc_start: 0.8702 (mttt) cc_final: 0.8148 (mtpt) REVERT: E 64 LYS cc_start: 0.7725 (mttt) cc_final: 0.7307 (mttt) REVERT: E 76 GLN cc_start: 0.8065 (tt0) cc_final: 0.7819 (tt0) REVERT: E 129 ARG cc_start: 0.8403 (tmt-80) cc_final: 0.7967 (tpt90) REVERT: F 25 ASN cc_start: 0.9069 (m-40) cc_final: 0.8772 (m110) REVERT: F 35 ARG cc_start: 0.8027 (mtp85) cc_final: 0.7666 (mtp85) REVERT: F 63 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8217 (mt-10) REVERT: F 91 LYS cc_start: 0.8737 (ttmt) cc_final: 0.8253 (ttpt) REVERT: G 61 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7760 (tp30) REVERT: G 64 GLU cc_start: 0.8191 (tp30) cc_final: 0.7862 (tm-30) REVERT: G 79 ILE cc_start: 0.8041 (tp) cc_final: 0.7841 (pt) REVERT: H 68 ASP cc_start: 0.8585 (t70) cc_final: 0.8063 (t0) REVERT: H 85 LYS cc_start: 0.8688 (mptm) cc_final: 0.8076 (mmtp) REVERT: H 93 GLU cc_start: 0.7969 (mp0) cc_final: 0.7546 (mp0) REVERT: S 172 LYS cc_start: 0.8186 (mmmt) cc_final: 0.7772 (mmmm) REVERT: S 173 GLN cc_start: 0.8054 (pm20) cc_final: 0.7798 (pm20) outliers start: 16 outliers final: 8 residues processed: 163 average time/residue: 0.3277 time to fit residues: 70.4329 Evaluate side-chains 156 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain S residue 168 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 0.0770 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 38 ASN F 75 HIS F 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12925 Z= 0.193 Angle : 0.543 6.496 18715 Z= 0.330 Chirality : 0.034 0.165 2131 Planarity : 0.004 0.037 1346 Dihedral : 30.433 156.921 4061 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.82 % Allowed : 13.93 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.31), residues: 747 helix: 1.66 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.32 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP S 164 HIS 0.004 0.001 HIS D 109 PHE 0.010 0.002 PHE E 67 TYR 0.011 0.001 TYR D 40 ARG 0.004 0.000 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.861 Fit side-chains REVERT: A 73 GLU cc_start: 0.7996 (tt0) cc_final: 0.7756 (tt0) REVERT: A 79 LYS cc_start: 0.7915 (tttp) cc_final: 0.7697 (tttt) REVERT: A 105 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7585 (mt-10) REVERT: A 115 LYS cc_start: 0.8985 (mttt) cc_final: 0.8749 (mmtt) REVERT: B 25 ASN cc_start: 0.7866 (m-40) cc_final: 0.7254 (m110) REVERT: B 63 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7859 (mt-10) REVERT: B 88 TYR cc_start: 0.8026 (m-10) cc_final: 0.7631 (m-80) REVERT: C 64 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7294 (tm-30) REVERT: C 95 LYS cc_start: 0.8983 (ttmp) cc_final: 0.8697 (tttt) REVERT: D 46 LYS cc_start: 0.8548 (mmpt) cc_final: 0.8226 (mmmt) REVERT: D 82 HIS cc_start: 0.8001 (m-70) cc_final: 0.7466 (m-70) REVERT: D 86 ARG cc_start: 0.8126 (mtp85) cc_final: 0.7833 (mmt90) REVERT: D 93 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7429 (mp0) REVERT: D 105 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7801 (mm-30) REVERT: D 108 LYS cc_start: 0.8661 (mttt) cc_final: 0.8133 (mtpt) REVERT: E 64 LYS cc_start: 0.7653 (mttt) cc_final: 0.7255 (mttt) REVERT: E 76 GLN cc_start: 0.8034 (tt0) cc_final: 0.7756 (tt0) REVERT: E 129 ARG cc_start: 0.8407 (tmt-80) cc_final: 0.7948 (tpt90) REVERT: F 35 ARG cc_start: 0.8043 (mtp85) cc_final: 0.7678 (mtp85) REVERT: F 91 LYS cc_start: 0.8646 (ttmt) cc_final: 0.8187 (ttpt) REVERT: G 35 ARG cc_start: 0.8276 (mtm110) cc_final: 0.8073 (ttm-80) REVERT: G 61 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7725 (tp30) REVERT: G 79 ILE cc_start: 0.7967 (tp) cc_final: 0.7728 (pt) REVERT: H 68 ASP cc_start: 0.8541 (t70) cc_final: 0.8007 (t0) REVERT: H 85 LYS cc_start: 0.8687 (mptm) cc_final: 0.8057 (mmtp) REVERT: H 93 GLU cc_start: 0.8242 (mp0) cc_final: 0.7991 (mp0) outliers start: 18 outliers final: 12 residues processed: 154 average time/residue: 0.3557 time to fit residues: 71.1465 Evaluate side-chains 154 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain S residue 168 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN H 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12925 Z= 0.192 Angle : 0.542 6.938 18715 Z= 0.330 Chirality : 0.034 0.154 2131 Planarity : 0.004 0.038 1346 Dihedral : 30.396 156.421 4061 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.44 % Allowed : 13.62 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.31), residues: 747 helix: 1.90 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.23 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP S 164 HIS 0.004 0.001 HIS D 109 PHE 0.012 0.001 PHE H 65 TYR 0.011 0.001 TYR D 40 ARG 0.003 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.906 Fit side-chains REVERT: A 59 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7166 (pm20) REVERT: A 79 LYS cc_start: 0.7919 (tttp) cc_final: 0.7703 (tttt) REVERT: A 105 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7565 (mt-10) REVERT: A 115 LYS cc_start: 0.9009 (mttt) cc_final: 0.8768 (mmtt) REVERT: B 59 LYS cc_start: 0.8138 (tttt) cc_final: 0.7910 (tttp) REVERT: B 63 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7862 (mt-10) REVERT: B 88 TYR cc_start: 0.8011 (m-10) cc_final: 0.7607 (m-80) REVERT: C 64 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7310 (tm-30) REVERT: C 95 LYS cc_start: 0.8967 (ttmp) cc_final: 0.8680 (tttt) REVERT: D 46 LYS cc_start: 0.8511 (mmpt) cc_final: 0.8172 (mmmt) REVERT: D 82 HIS cc_start: 0.8003 (m-70) cc_final: 0.7436 (m-70) REVERT: D 86 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7851 (mmt90) REVERT: D 93 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7398 (mp0) REVERT: D 105 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7769 (mm-30) REVERT: D 108 LYS cc_start: 0.8657 (mttt) cc_final: 0.8138 (mtpt) REVERT: E 64 LYS cc_start: 0.7653 (mttt) cc_final: 0.7257 (mttt) REVERT: E 76 GLN cc_start: 0.8051 (tt0) cc_final: 0.7749 (tt0) REVERT: E 129 ARG cc_start: 0.8376 (tmt-80) cc_final: 0.8049 (tpt90) REVERT: F 25 ASN cc_start: 0.8971 (m-40) cc_final: 0.8688 (m110) REVERT: F 35 ARG cc_start: 0.8056 (mtp85) cc_final: 0.7685 (mtp85) REVERT: F 63 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8215 (mt-10) REVERT: F 91 LYS cc_start: 0.8653 (ttmt) cc_final: 0.8188 (ttpt) REVERT: G 35 ARG cc_start: 0.8272 (mtm110) cc_final: 0.8071 (ttm-80) REVERT: G 61 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7775 (tp30) REVERT: G 64 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7883 (tm-30) REVERT: G 79 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7728 (pt) REVERT: H 68 ASP cc_start: 0.8566 (t70) cc_final: 0.8039 (t0) REVERT: H 85 LYS cc_start: 0.8699 (mptm) cc_final: 0.8387 (mmtt) REVERT: H 93 GLU cc_start: 0.8207 (mp0) cc_final: 0.7928 (mp0) REVERT: S 172 LYS cc_start: 0.8194 (mmmt) cc_final: 0.7936 (mmmm) outliers start: 22 outliers final: 11 residues processed: 156 average time/residue: 0.3523 time to fit residues: 71.3090 Evaluate side-chains 157 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain S residue 168 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12925 Z= 0.205 Angle : 0.547 7.152 18715 Z= 0.330 Chirality : 0.034 0.155 2131 Planarity : 0.004 0.037 1346 Dihedral : 30.443 155.585 4061 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.97 % Allowed : 14.08 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.31), residues: 747 helix: 1.99 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.16 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 164 HIS 0.004 0.001 HIS D 109 PHE 0.012 0.002 PHE H 65 TYR 0.012 0.001 TYR D 40 ARG 0.003 0.000 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.882 Fit side-chains REVERT: A 59 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7200 (pm20) REVERT: A 73 GLU cc_start: 0.8123 (tt0) cc_final: 0.7352 (tt0) REVERT: A 79 LYS cc_start: 0.7942 (tttp) cc_final: 0.7728 (tttt) REVERT: A 105 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7447 (mt-10) REVERT: A 115 LYS cc_start: 0.8995 (mttt) cc_final: 0.8767 (mmtt) REVERT: B 25 ASN cc_start: 0.8220 (m-40) cc_final: 0.7388 (m110) REVERT: B 63 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7861 (mt-10) REVERT: B 88 TYR cc_start: 0.8225 (m-10) cc_final: 0.7822 (m-80) REVERT: C 64 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7311 (tm-30) REVERT: C 95 LYS cc_start: 0.8971 (ttmp) cc_final: 0.8692 (tttt) REVERT: D 46 LYS cc_start: 0.8504 (mmpt) cc_final: 0.8164 (mmmt) REVERT: D 71 GLU cc_start: 0.8403 (tp30) cc_final: 0.7887 (mm-30) REVERT: D 82 HIS cc_start: 0.7996 (m-70) cc_final: 0.7408 (m-70) REVERT: D 86 ARG cc_start: 0.8126 (mtp85) cc_final: 0.7792 (mmt90) REVERT: D 105 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7836 (mm-30) REVERT: D 108 LYS cc_start: 0.8660 (mttt) cc_final: 0.8138 (mtpt) REVERT: E 64 LYS cc_start: 0.7687 (mttt) cc_final: 0.7294 (mttt) REVERT: E 76 GLN cc_start: 0.8142 (tt0) cc_final: 0.7836 (tt0) REVERT: E 129 ARG cc_start: 0.8379 (tmt-80) cc_final: 0.8045 (tpt90) REVERT: F 35 ARG cc_start: 0.8046 (mtp85) cc_final: 0.7659 (mtp85) REVERT: F 74 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7912 (mt-10) REVERT: F 91 LYS cc_start: 0.8725 (ttmt) cc_final: 0.8254 (ttpt) REVERT: G 79 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7712 (pt) REVERT: H 68 ASP cc_start: 0.8564 (t70) cc_final: 0.8075 (t0) REVERT: H 85 LYS cc_start: 0.8712 (mptm) cc_final: 0.8394 (mmtt) REVERT: H 108 LYS cc_start: 0.8961 (mmtp) cc_final: 0.8709 (mttm) outliers start: 19 outliers final: 13 residues processed: 154 average time/residue: 0.3490 time to fit residues: 69.6754 Evaluate side-chains 157 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain S residue 168 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12925 Z= 0.196 Angle : 0.552 10.492 18715 Z= 0.331 Chirality : 0.034 0.187 2131 Planarity : 0.004 0.039 1346 Dihedral : 30.426 155.632 4061 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.35 % Allowed : 14.71 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.31), residues: 747 helix: 2.10 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.16 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 164 HIS 0.008 0.001 HIS G 31 PHE 0.012 0.001 PHE H 65 TYR 0.009 0.001 TYR D 40 ARG 0.006 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.896 Fit side-chains REVERT: A 59 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7199 (pm20) REVERT: A 79 LYS cc_start: 0.7943 (tttp) cc_final: 0.7726 (tttt) REVERT: A 105 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7447 (mt-10) REVERT: A 115 LYS cc_start: 0.8993 (mttt) cc_final: 0.8765 (mmtt) REVERT: B 25 ASN cc_start: 0.8136 (m-40) cc_final: 0.7517 (m110) REVERT: B 63 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7860 (mt-10) REVERT: B 88 TYR cc_start: 0.8073 (m-10) cc_final: 0.7668 (m-80) REVERT: C 64 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7314 (tm-30) REVERT: C 95 LYS cc_start: 0.8969 (ttmp) cc_final: 0.8687 (tttt) REVERT: D 46 LYS cc_start: 0.8474 (mmpt) cc_final: 0.8136 (mmmt) REVERT: D 71 GLU cc_start: 0.8402 (tp30) cc_final: 0.7881 (mm-30) REVERT: D 82 HIS cc_start: 0.7990 (m-70) cc_final: 0.7389 (m-70) REVERT: D 86 ARG cc_start: 0.8118 (mtp85) cc_final: 0.7883 (mmt90) REVERT: D 105 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7845 (mm-30) REVERT: D 108 LYS cc_start: 0.8655 (mttt) cc_final: 0.8142 (mtpt) REVERT: E 64 LYS cc_start: 0.7668 (mttt) cc_final: 0.7266 (mttt) REVERT: E 73 GLU cc_start: 0.8118 (pt0) cc_final: 0.7605 (pt0) REVERT: E 76 GLN cc_start: 0.8139 (tt0) cc_final: 0.7836 (tt0) REVERT: E 129 ARG cc_start: 0.8367 (tmt-80) cc_final: 0.8073 (tpt90) REVERT: F 25 ASN cc_start: 0.8945 (m-40) cc_final: 0.8630 (m-40) REVERT: F 35 ARG cc_start: 0.8046 (mtp85) cc_final: 0.7655 (mtp85) REVERT: F 91 LYS cc_start: 0.8679 (ttmt) cc_final: 0.8200 (ttpt) REVERT: G 79 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7714 (pt) REVERT: H 68 ASP cc_start: 0.8558 (t70) cc_final: 0.8069 (t0) REVERT: H 85 LYS cc_start: 0.8711 (mptm) cc_final: 0.8392 (mmtt) REVERT: H 108 LYS cc_start: 0.8954 (mmtp) cc_final: 0.8709 (mttm) REVERT: S 172 LYS cc_start: 0.8326 (mmmt) cc_final: 0.7866 (mmmm) outliers start: 15 outliers final: 10 residues processed: 149 average time/residue: 0.3304 time to fit residues: 64.7942 Evaluate side-chains 155 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 38 ASN F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 12925 Z= 0.342 Angle : 0.610 9.140 18715 Z= 0.361 Chirality : 0.038 0.166 2131 Planarity : 0.005 0.039 1346 Dihedral : 30.695 155.141 4061 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.82 % Allowed : 14.40 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.30), residues: 747 helix: 1.77 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -1.34 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 164 HIS 0.006 0.001 HIS D 109 PHE 0.019 0.002 PHE C 25 TYR 0.010 0.001 TYR H 37 ARG 0.005 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 1.129 Fit side-chains REVERT: A 59 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7236 (pm20) REVERT: A 79 LYS cc_start: 0.7932 (tttp) cc_final: 0.7728 (tttt) REVERT: A 105 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7575 (mt-10) REVERT: B 25 ASN cc_start: 0.8182 (m-40) cc_final: 0.7639 (m110) REVERT: B 63 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7841 (mt-10) REVERT: C 64 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7303 (tm-30) REVERT: C 95 LYS cc_start: 0.8900 (ttmp) cc_final: 0.8630 (tttt) REVERT: D 71 GLU cc_start: 0.8381 (tp30) cc_final: 0.7850 (mm-30) REVERT: D 86 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7712 (mmt90) REVERT: D 105 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7739 (mm-30) REVERT: D 108 LYS cc_start: 0.8675 (mttt) cc_final: 0.8118 (mtpt) REVERT: F 35 ARG cc_start: 0.7982 (mtp85) cc_final: 0.7623 (mtp85) REVERT: F 74 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7946 (mt-10) REVERT: F 91 LYS cc_start: 0.8752 (ttmt) cc_final: 0.8299 (ttpt) REVERT: G 64 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7846 (tm-30) REVERT: G 79 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7825 (pt) REVERT: H 68 ASP cc_start: 0.8560 (t70) cc_final: 0.8134 (t0) REVERT: H 85 LYS cc_start: 0.8704 (mptm) cc_final: 0.8034 (mmtp) REVERT: H 108 LYS cc_start: 0.8880 (mmtp) cc_final: 0.8618 (mttm) REVERT: S 172 LYS cc_start: 0.8362 (mmmt) cc_final: 0.7931 (mmmm) outliers start: 18 outliers final: 12 residues processed: 149 average time/residue: 0.3449 time to fit residues: 67.5135 Evaluate side-chains 152 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 100 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12925 Z= 0.206 Angle : 0.568 8.344 18715 Z= 0.341 Chirality : 0.035 0.161 2131 Planarity : 0.004 0.040 1346 Dihedral : 30.640 155.260 4061 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.19 % Allowed : 15.18 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.31), residues: 747 helix: 1.98 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.26 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP S 164 HIS 0.004 0.001 HIS D 109 PHE 0.013 0.002 PHE H 65 TYR 0.024 0.001 TYR C 39 ARG 0.004 0.000 ARG G 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 1.171 Fit side-chains REVERT: A 59 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7261 (pm20) REVERT: A 79 LYS cc_start: 0.7869 (tttp) cc_final: 0.7649 (tttt) REVERT: A 105 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7542 (mt-10) REVERT: A 115 LYS cc_start: 0.8994 (mttt) cc_final: 0.8769 (mmtt) REVERT: B 25 ASN cc_start: 0.8195 (m-40) cc_final: 0.7680 (m110) REVERT: B 63 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7859 (mt-10) REVERT: C 64 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7281 (tm-30) REVERT: C 95 LYS cc_start: 0.8980 (ttmp) cc_final: 0.8708 (tttt) REVERT: D 71 GLU cc_start: 0.8373 (tp30) cc_final: 0.7835 (mm-30) REVERT: D 86 ARG cc_start: 0.7994 (mtp85) cc_final: 0.7587 (mmt90) REVERT: D 105 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7727 (mm-30) REVERT: D 108 LYS cc_start: 0.8684 (mttt) cc_final: 0.8138 (mtpt) REVERT: E 129 ARG cc_start: 0.8397 (tmt-80) cc_final: 0.8065 (tpt90) REVERT: F 35 ARG cc_start: 0.7973 (mtp85) cc_final: 0.7547 (mtp85) REVERT: F 74 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7937 (mt-10) REVERT: F 91 LYS cc_start: 0.8703 (ttmt) cc_final: 0.8241 (ttpt) REVERT: G 64 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7702 (tm-30) REVERT: G 79 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7783 (pt) REVERT: H 68 ASP cc_start: 0.8554 (t70) cc_final: 0.8099 (t0) REVERT: H 85 LYS cc_start: 0.8704 (mptm) cc_final: 0.8398 (mmtt) REVERT: H 108 LYS cc_start: 0.8865 (mmtp) cc_final: 0.8605 (mttm) REVERT: S 172 LYS cc_start: 0.8309 (mmmt) cc_final: 0.7876 (mmmm) outliers start: 14 outliers final: 10 residues processed: 146 average time/residue: 0.3440 time to fit residues: 66.2444 Evaluate side-chains 150 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.089771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.059136 restraints weight = 26284.683| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 1.63 r_work: 0.2692 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12925 Z= 0.197 Angle : 0.561 8.394 18715 Z= 0.337 Chirality : 0.034 0.159 2131 Planarity : 0.004 0.038 1346 Dihedral : 30.590 155.246 4061 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.03 % Allowed : 15.96 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.31), residues: 747 helix: 2.06 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.23 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 164 HIS 0.004 0.001 HIS D 109 PHE 0.012 0.002 PHE H 65 TYR 0.010 0.001 TYR D 40 ARG 0.004 0.000 ARG G 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2537.14 seconds wall clock time: 46 minutes 49.17 seconds (2809.17 seconds total)