Starting phenix.real_space_refine on Tue Jun 10 18:27:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hr1_34956/06_2025/8hr1_34956.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hr1_34956/06_2025/8hr1_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_34956/06_2025/8hr1_34956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hr1_34956/06_2025/8hr1_34956.map" model { file = "/net/cci-nas-00/data/ceres_data/8hr1_34956/06_2025/8hr1_34956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hr1_34956/06_2025/8hr1_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.63, per 1000 atoms: 0.63 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: 2.93 Conformation dependent library (CDL) restraints added in 959.3 milliseconds 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: 6.37 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: 4.43 Time building geometry restraints manager: 3.31 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: 1.090 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.890 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.280 ------------------------------------------------------------------------------- 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= 0.433 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 Details of bonding type rmsd hydrogen bonds : bond 0.32606 ( 680) hydrogen bonds : angle 9.58888 ( 1634) covalent geometry : bond 0.00972 (12925) covalent geometry : angle 0.80288 (18715) *********************** 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 : 0.993 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: 0.4349 time to fit residues: 122.7717 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 : 0.902 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.089786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.060691 restraints weight = 27274.574| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.65 r_work: 0.2758 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 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= 0.183 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 Details of bonding type rmsd hydrogen bonds : bond 0.09737 ( 680) hydrogen bonds : angle 3.48692 ( 1634) covalent geometry : bond 0.00401 (12925) covalent geometry : angle 0.62683 (18715) *********************** 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 : 0.956 Fit side-chains REVERT: A 79 LYS cc_start: 0.8567 (tttp) cc_final: 0.8329 (tttt) REVERT: A 93 GLN cc_start: 0.9247 (OUTLIER) cc_final: 0.8929 (tt0) REVERT: D 46 LYS cc_start: 0.8899 (mmpt) cc_final: 0.8689 (mmmt) REVERT: D 86 ARG cc_start: 0.8745 (mtp85) cc_final: 0.8432 (mmt90) REVERT: D 105 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8165 (mm-30) REVERT: D 108 LYS cc_start: 0.8948 (mttt) cc_final: 0.8672 (mtpp) REVERT: E 41 TYR cc_start: 0.8438 (m-80) cc_final: 0.8179 (m-10) REVERT: E 73 GLU cc_start: 0.8825 (pt0) cc_final: 0.8525 (pt0) REVERT: E 76 GLN cc_start: 0.8752 (tt0) cc_final: 0.8514 (tt0) REVERT: E 79 LYS cc_start: 0.8225 (tttp) cc_final: 0.7672 (ttpt) REVERT: F 35 ARG cc_start: 0.8953 (mtp85) cc_final: 0.8663 (mtp85) REVERT: F 91 LYS cc_start: 0.9181 (ttmt) cc_final: 0.8838 (ttpt) REVERT: G 13 LYS cc_start: 0.5890 (OUTLIER) cc_final: 0.5564 (pttm) REVERT: H 85 LYS cc_start: 0.8901 (mptm) cc_final: 0.8696 (mmtt) REVERT: S 172 LYS cc_start: 0.7885 (mmmt) cc_final: 0.7599 (mmmm) outliers start: 14 outliers final: 5 residues processed: 193 average time/residue: 0.3541 time to fit residues: 87.9983 Evaluate side-chains 146 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN 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 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 28 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 D 82 HIS E 68 GLN E 93 GLN F 93 GLN G 68 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.089202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.059163 restraints weight = 27396.878| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.61 r_work: 0.2706 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3700 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= 0.188 Angle : 0.585 6.618 18715 Z= 0.352 Chirality : 0.035 0.131 2131 Planarity : 0.005 0.079 1346 Dihedral : 30.271 163.931 4061 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.50 % Allowed : 13.62 % Favored : 83.88 % 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: 0.06 (0.30), residues: 747 helix: 0.67 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.54 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.006 TRP S 164 HIS 0.009 0.002 HIS C 31 PHE 0.017 0.002 PHE G 25 TYR 0.013 0.002 TYR D 40 ARG 0.023 0.001 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.08980 ( 680) hydrogen bonds : angle 3.03560 ( 1634) covalent geometry : bond 0.00421 (12925) covalent geometry : angle 0.58505 (18715) *********************** 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 174 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 1.005 Fit side-chains REVERT: A 79 LYS cc_start: 0.8566 (tttp) cc_final: 0.8299 (tttt) REVERT: A 93 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8780 (tt0) REVERT: D 46 LYS cc_start: 0.8862 (mmpt) cc_final: 0.8578 (mmmt) REVERT: D 86 ARG cc_start: 0.8793 (mtp85) cc_final: 0.8463 (mmt90) REVERT: D 105 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8367 (mm-30) REVERT: D 108 LYS cc_start: 0.9124 (mttt) cc_final: 0.8859 (mtpt) REVERT: E 41 TYR cc_start: 0.8558 (m-80) cc_final: 0.8227 (m-10) REVERT: E 64 LYS cc_start: 0.8999 (mttt) cc_final: 0.8688 (mttt) REVERT: E 73 GLU cc_start: 0.8913 (pt0) cc_final: 0.8700 (pt0) REVERT: E 93 GLN cc_start: 0.8973 (tp-100) cc_final: 0.8713 (tt0) REVERT: F 91 LYS cc_start: 0.9231 (ttmt) cc_final: 0.8948 (ttpt) REVERT: G 13 LYS cc_start: 0.5950 (OUTLIER) cc_final: 0.5549 (pttm) REVERT: H 85 LYS cc_start: 0.8941 (mptm) cc_final: 0.8417 (mmtp) outliers start: 16 outliers final: 7 residues processed: 166 average time/residue: 0.3092 time to fit residues: 68.6120 Evaluate side-chains 154 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 98 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 25 ASN C 38 ASN D 82 HIS F 75 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.086743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.055963 restraints weight = 26844.004| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 1.67 r_work: 0.2617 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 12925 Z= 0.337 Angle : 0.682 7.090 18715 Z= 0.398 Chirality : 0.043 0.165 2131 Planarity : 0.006 0.050 1346 Dihedral : 30.892 157.562 4061 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.29 % Allowed : 15.18 % Favored : 81.53 % 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: 0.18 (0.29), residues: 747 helix: 0.79 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -1.63 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP S 164 HIS 0.014 0.003 HIS C 31 PHE 0.028 0.003 PHE A 84 TYR 0.013 0.002 TYR D 40 ARG 0.006 0.001 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.09367 ( 680) hydrogen bonds : angle 3.29353 ( 1634) covalent geometry : bond 0.00775 (12925) covalent geometry : angle 0.68160 (18715) *********************** 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 160 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 1.234 Fit side-chains REVERT: A 79 LYS cc_start: 0.8589 (tttp) cc_final: 0.8367 (tttt) REVERT: C 64 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8349 (tm-30) REVERT: D 105 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8277 (mm-30) REVERT: D 108 LYS cc_start: 0.9137 (mttt) cc_final: 0.8784 (mtpt) REVERT: E 41 TYR cc_start: 0.8635 (m-80) cc_final: 0.8371 (m-10) REVERT: E 64 LYS cc_start: 0.9089 (mttt) cc_final: 0.8807 (mttt) REVERT: E 93 GLN cc_start: 0.9160 (tp-100) cc_final: 0.8843 (tt0) REVERT: E 97 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8497 (mt-10) REVERT: F 91 LYS cc_start: 0.9325 (ttmt) cc_final: 0.9061 (ttpt) REVERT: H 85 LYS cc_start: 0.9005 (mptm) cc_final: 0.8473 (mmtp) REVERT: H 93 GLU cc_start: 0.8734 (mp0) cc_final: 0.8335 (mp0) REVERT: S 172 LYS cc_start: 0.8090 (mmmt) cc_final: 0.7684 (mmmm) REVERT: S 173 GLN cc_start: 0.8136 (pm20) cc_final: 0.7852 (pm20) outliers start: 21 outliers final: 14 residues processed: 152 average time/residue: 0.3483 time to fit residues: 70.4327 Evaluate side-chains 149 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 123 SER 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 101 THR Chi-restraints excluded: chain H residue 122 THR 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 86 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN D 82 HIS F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.089084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.058595 restraints weight = 26940.384| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.60 r_work: 0.2685 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12925 Z= 0.162 Angle : 0.564 6.778 18715 Z= 0.342 Chirality : 0.035 0.126 2131 Planarity : 0.004 0.043 1346 Dihedral : 30.641 157.652 4061 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.97 % Allowed : 15.34 % Favored : 81.69 % 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: 1.03 (0.30), residues: 747 helix: 1.46 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.44 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP S 164 HIS 0.003 0.001 HIS D 109 PHE 0.012 0.002 PHE E 67 TYR 0.013 0.001 TYR D 40 ARG 0.003 0.000 ARG G 35 Details of bonding type rmsd hydrogen bonds : bond 0.08837 ( 680) hydrogen bonds : angle 2.83709 ( 1634) covalent geometry : bond 0.00358 (12925) covalent geometry : angle 0.56428 (18715) *********************** 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 162 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.892 Fit side-chains REVERT: A 59 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.7987 (pm20) REVERT: A 79 LYS cc_start: 0.8591 (tttp) cc_final: 0.8388 (tttt) REVERT: C 56 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8433 (tt0) REVERT: C 64 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8302 (tm-30) REVERT: D 93 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8400 (mp0) REVERT: D 105 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8244 (mm-30) REVERT: D 108 LYS cc_start: 0.9079 (mttt) cc_final: 0.8794 (mtpt) REVERT: E 41 TYR cc_start: 0.8721 (m-80) cc_final: 0.8458 (m-10) REVERT: E 64 LYS cc_start: 0.9007 (mttt) cc_final: 0.8701 (mttt) REVERT: E 97 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8442 (mt-10) REVERT: F 91 LYS cc_start: 0.9259 (ttmt) cc_final: 0.8969 (ttpt) REVERT: G 64 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8416 (tm-30) REVERT: H 85 LYS cc_start: 0.9005 (mptm) cc_final: 0.8443 (mmtp) outliers start: 19 outliers final: 12 residues processed: 151 average time/residue: 0.3082 time to fit residues: 62.1433 Evaluate side-chains 150 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain S residue 165 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 43 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 D 82 HIS H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.088188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.057389 restraints weight = 27287.502| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 1.61 r_work: 0.2653 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12925 Z= 0.221 Angle : 0.592 7.962 18715 Z= 0.354 Chirality : 0.037 0.130 2131 Planarity : 0.004 0.043 1346 Dihedral : 30.707 156.276 4061 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.29 % Allowed : 15.18 % Favored : 81.53 % 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: 1.17 (0.30), residues: 747 helix: 1.58 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.42 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP S 164 HIS 0.006 0.001 HIS C 31 PHE 0.016 0.002 PHE G 25 TYR 0.011 0.001 TYR D 40 ARG 0.004 0.001 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.08709 ( 680) hydrogen bonds : angle 2.91385 ( 1634) covalent geometry : bond 0.00505 (12925) covalent geometry : angle 0.59162 (18715) *********************** 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 159 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 1.004 Fit side-chains REVERT: A 59 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8039 (pm20) REVERT: B 88 TYR cc_start: 0.9135 (m-10) cc_final: 0.8735 (m-80) REVERT: C 64 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8327 (tm-30) REVERT: D 105 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8367 (mm-30) REVERT: D 108 LYS cc_start: 0.9121 (mttt) cc_final: 0.8825 (mtpt) REVERT: E 41 TYR cc_start: 0.8709 (m-80) cc_final: 0.8506 (m-10) REVERT: E 64 LYS cc_start: 0.9029 (mttt) cc_final: 0.8708 (mttt) REVERT: E 97 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8491 (mt-10) REVERT: F 91 LYS cc_start: 0.9306 (ttmt) cc_final: 0.9005 (ttpt) REVERT: G 64 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8470 (tm-30) REVERT: H 84 ASN cc_start: 0.9146 (OUTLIER) cc_final: 0.8933 (m-40) REVERT: H 85 LYS cc_start: 0.9014 (mptm) cc_final: 0.8420 (mmtp) REVERT: H 93 GLU cc_start: 0.8781 (mp0) cc_final: 0.8492 (mp0) REVERT: S 172 LYS cc_start: 0.8074 (mmmt) cc_final: 0.7657 (mmmm) REVERT: S 173 GLN cc_start: 0.7901 (pm20) cc_final: 0.7663 (pm20) outliers start: 21 outliers final: 14 residues processed: 146 average time/residue: 0.3190 time to fit residues: 61.8523 Evaluate side-chains 151 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR 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 D residue 101 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 76 GLN 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 101 THR Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain S residue 165 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 33 optimal weight: 0.0970 chunk 75 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN D 82 HIS H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.089249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.058642 restraints weight = 27014.062| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.60 r_work: 0.2683 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12925 Z= 0.154 Angle : 0.559 7.520 18715 Z= 0.339 Chirality : 0.034 0.127 2131 Planarity : 0.004 0.043 1346 Dihedral : 30.673 156.415 4061 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.03 % Allowed : 16.28 % Favored : 81.69 % 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: 1.51 (0.30), residues: 747 helix: 1.84 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.33 (0.41), 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 0.011 0.001 PHE E 67 TYR 0.012 0.001 TYR D 40 ARG 0.004 0.000 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.08578 ( 680) hydrogen bonds : angle 2.77902 ( 1634) covalent geometry : bond 0.00338 (12925) covalent geometry : angle 0.55868 (18715) *********************** 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 156 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.980 Fit side-chains REVERT: A 59 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: B 88 TYR cc_start: 0.9111 (m-10) cc_final: 0.8727 (m-80) REVERT: C 64 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8308 (tm-30) REVERT: D 105 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8332 (mm-30) REVERT: D 108 LYS cc_start: 0.9096 (mttt) cc_final: 0.8829 (mtpt) REVERT: E 41 TYR cc_start: 0.8716 (m-80) cc_final: 0.8478 (m-10) REVERT: E 64 LYS cc_start: 0.9002 (mttt) cc_final: 0.8671 (mttt) REVERT: E 97 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8446 (mt-10) REVERT: F 91 LYS cc_start: 0.9293 (ttmt) cc_final: 0.8984 (ttpt) REVERT: G 64 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8461 (tm-30) REVERT: H 85 LYS cc_start: 0.8962 (mptm) cc_final: 0.8377 (mmtp) REVERT: H 93 GLU cc_start: 0.8732 (mp0) cc_final: 0.8422 (mp0) REVERT: S 172 LYS cc_start: 0.7981 (mmmt) cc_final: 0.7642 (mmmm) REVERT: S 173 GLN cc_start: 0.7884 (pm20) cc_final: 0.7673 (pm20) outliers start: 13 outliers final: 10 residues processed: 148 average time/residue: 0.3085 time to fit residues: 61.0895 Evaluate side-chains 149 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 101 THR 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 75 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 11 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 C 38 ASN D 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.087604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.056483 restraints weight = 26735.478| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.67 r_work: 0.2626 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 12925 Z= 0.260 Angle : 0.610 7.708 18715 Z= 0.362 Chirality : 0.038 0.135 2131 Planarity : 0.005 0.043 1346 Dihedral : 30.925 155.163 4061 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.97 % Allowed : 14.87 % Favored : 82.16 % 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: 1.27 (0.30), residues: 747 helix: 1.67 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.45 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 164 HIS 0.006 0.002 HIS D 109 PHE 0.016 0.002 PHE G 25 TYR 0.010 0.002 TYR C 57 ARG 0.006 0.001 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.08770 ( 680) hydrogen bonds : angle 2.98280 ( 1634) covalent geometry : bond 0.00598 (12925) covalent geometry : angle 0.61041 (18715) *********************** 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 156 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 1.017 Fit side-chains REVERT: A 59 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: C 64 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8356 (tm-30) REVERT: D 71 GLU cc_start: 0.8959 (tp30) cc_final: 0.8668 (mm-30) REVERT: D 105 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8306 (mm-30) REVERT: D 108 LYS cc_start: 0.9142 (mttt) cc_final: 0.8805 (mtpt) REVERT: E 64 LYS cc_start: 0.9033 (mttt) cc_final: 0.8702 (mttt) REVERT: E 97 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8574 (mt-10) REVERT: F 91 LYS cc_start: 0.9352 (ttmt) cc_final: 0.9015 (ttpt) REVERT: G 64 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8393 (tm-30) REVERT: H 93 GLU cc_start: 0.8866 (mp0) cc_final: 0.8491 (mp0) outliers start: 19 outliers final: 16 residues processed: 147 average time/residue: 0.3362 time to fit residues: 64.9432 Evaluate side-chains 151 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 D residue 113 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 76 GLN 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 101 THR Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 88 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN D 82 HIS F 93 GLN H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.088169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.057136 restraints weight = 26468.808| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.65 r_work: 0.2643 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.4347 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= 0.196 Angle : 0.589 8.278 18715 Z= 0.352 Chirality : 0.036 0.127 2131 Planarity : 0.004 0.044 1346 Dihedral : 30.912 155.239 4061 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.82 % Allowed : 15.02 % Favored : 82.16 % 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: 1.38 (0.30), residues: 747 helix: 1.75 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.41 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP S 164 HIS 0.005 0.001 HIS D 109 PHE 0.012 0.002 PHE G 25 TYR 0.013 0.001 TYR D 40 ARG 0.003 0.001 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.08671 ( 680) hydrogen bonds : angle 2.92646 ( 1634) covalent geometry : bond 0.00442 (12925) covalent geometry : angle 0.58882 (18715) *********************** 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 154 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.986 Fit side-chains REVERT: A 59 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8046 (pm20) REVERT: C 64 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8366 (tm-30) REVERT: D 71 GLU cc_start: 0.8951 (tp30) cc_final: 0.8651 (mm-30) REVERT: D 105 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8279 (mm-30) REVERT: D 108 LYS cc_start: 0.9131 (mttt) cc_final: 0.8792 (mtpt) REVERT: E 64 LYS cc_start: 0.9015 (mttt) cc_final: 0.8678 (mttt) REVERT: E 97 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8562 (mt-10) REVERT: F 91 LYS cc_start: 0.9341 (ttmt) cc_final: 0.9001 (ttpt) REVERT: G 64 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8390 (tm-30) REVERT: H 93 GLU cc_start: 0.8864 (mp0) cc_final: 0.8478 (mp0) outliers start: 18 outliers final: 14 residues processed: 143 average time/residue: 0.3223 time to fit residues: 61.2653 Evaluate side-chains 148 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 D residue 113 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain S residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 51 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 98 optimal weight: 4.9990 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 D 47 GLN D 82 HIS H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.088605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.057701 restraints weight = 26578.873| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.63 r_work: 0.2662 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12925 Z= 0.165 Angle : 0.585 13.764 18715 Z= 0.349 Chirality : 0.035 0.158 2131 Planarity : 0.004 0.043 1346 Dihedral : 30.866 155.306 4061 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.66 % Allowed : 15.65 % Favored : 81.69 % 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: 1.58 (0.30), residues: 747 helix: 1.90 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.33 (0.40), 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 0.011 0.002 PHE E 67 TYR 0.013 0.001 TYR D 40 ARG 0.003 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.08574 ( 680) hydrogen bonds : angle 2.84469 ( 1634) covalent geometry : bond 0.00369 (12925) covalent geometry : angle 0.58502 (18715) ********************** 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 156 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.912 Fit side-chains REVERT: A 59 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8068 (pm20) REVERT: C 64 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8367 (tm-30) REVERT: D 71 GLU cc_start: 0.8886 (tp30) cc_final: 0.8616 (mm-30) REVERT: D 105 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8217 (mm-30) REVERT: D 108 LYS cc_start: 0.9082 (mttt) cc_final: 0.8795 (mtpt) REVERT: E 64 LYS cc_start: 0.9016 (mttt) cc_final: 0.8692 (mttt) REVERT: E 97 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8501 (mt-10) REVERT: F 91 LYS cc_start: 0.9324 (ttmt) cc_final: 0.8995 (ttpt) REVERT: G 64 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8412 (tm-30) REVERT: H 93 GLU cc_start: 0.8798 (mp0) cc_final: 0.8439 (mp0) outliers start: 17 outliers final: 13 residues processed: 145 average time/residue: 0.3351 time to fit residues: 65.1795 Evaluate side-chains 149 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 61 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 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 56 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN D 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.088441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.057830 restraints weight = 26844.124| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.62 r_work: 0.2670 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12925 Z= 0.182 Angle : 0.571 8.695 18715 Z= 0.342 Chirality : 0.035 0.128 2131 Planarity : 0.004 0.043 1346 Dihedral : 30.728 155.024 4061 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.50 % Allowed : 15.49 % 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: 1.71 (0.30), residues: 747 helix: 2.00 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.30 (0.41), 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 0.013 0.001 TYR D 40 ARG 0.003 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.08521 ( 680) hydrogen bonds : angle 2.78691 ( 1634) covalent geometry : bond 0.00411 (12925) covalent geometry : angle 0.57078 (18715) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7324.71 seconds wall clock time: 125 minutes 28.10 seconds (7528.10 seconds total)