Starting phenix.real_space_refine on Wed Aug 5 23:22:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9geo_51296/08_2026/9geo_51296.cif Found real_map, /net/cci-nas-00/data/ceres_data/9geo_51296/08_2026/9geo_51296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9geo_51296/08_2026/9geo_51296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9geo_51296/08_2026/9geo_51296.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9geo_51296/08_2026/9geo_51296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9geo_51296/08_2026/9geo_51296.map" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 1.000 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 290 5.49 5 S 12 5.16 5 C 6598 2.51 5 N 2248 2.21 5 O 3052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12200 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" 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: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Time building chain proxies: 2.08, per 1000 atoms: 0.17 Number of scatterers: 12200 At special positions: 0 Unit cell: (73.44, 114.24, 121.04, 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 12 16.00 P 290 15.00 O 3052 8.00 N 2248 7.00 C 6598 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: 0.79 Conformation dependent library (CDL) restraints added in 311.1 milliseconds 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1418 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 72.9% alpha, 3.2% beta 137 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.779A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.542A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.527A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.800A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.691A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.510A 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 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.751A 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 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.079A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.763A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.961A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.052A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 411 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 350 hydrogen bonds 700 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 1.10 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: 2217 1.33 - 1.45: 4170 1.45 - 1.57: 5762 1.57 - 1.69: 578 1.69 - 1.81: 22 Bond restraints: 12749 Sorted by residual: bond pdb=" C3' DA I -1 " pdb=" C2' DA I -1 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DC I 1 " pdb=" C2' DC I 1 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DC I 40 " pdb=" C2' DC I 40 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.72e+00 bond pdb=" C3' DG J 52 " pdb=" C2' DG J 52 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.18e+00 bond pdb=" C3' DA J 63 " pdb=" C2' DA J 63 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.77e+00 ... (remaining 12744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 15855 1.00 - 1.99: 1927 1.99 - 2.99: 620 2.99 - 3.99: 49 3.99 - 4.98: 10 Bond angle restraints: 18461 Sorted by residual: angle pdb=" O4' DA I -68 " pdb=" C1' DA I -68 " pdb=" N9 DA I -68 " ideal model delta sigma weight residual 108.00 111.15 -3.15 7.00e-01 2.04e+00 2.02e+01 angle pdb=" N3 DT I -61 " pdb=" C4 DT I -61 " pdb=" O4 DT I -61 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT I -50 " pdb=" C4 DT I -50 " pdb=" O4 DT I -50 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT I 9 " pdb=" C4 DT I 9 " pdb=" O4 DT I 9 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT J 31 " pdb=" C4 DT J 31 " pdb=" O4 DT J 31 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 ... (remaining 18456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.83: 5375 33.83 - 67.67: 1525 67.67 - 101.50: 21 101.50 - 135.33: 1 135.33 - 169.16: 2 Dihedral angle restraints: 6924 sinusoidal: 4728 harmonic: 2196 Sorted by residual: dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 50.84 169.16 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DC J 51 " pdb=" C3' DC J 51 " pdb=" O3' DC J 51 " pdb=" P DG J 52 " ideal model delta sinusoidal sigma weight residual 220.00 70.41 149.59 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 91.33 128.67 1 3.50e+01 8.16e-04 1.27e+01 ... (remaining 6921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1134 0.030 - 0.060: 624 0.060 - 0.091: 232 0.091 - 0.121: 103 0.121 - 0.151: 10 Chirality restraints: 2103 Sorted by residual: chirality pdb=" CA PRO A 43 " pdb=" N PRO A 43 " pdb=" C PRO A 43 " pdb=" CB PRO A 43 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" C3' DG I 20 " pdb=" C4' DG I 20 " pdb=" O3' DG I 20 " pdb=" C2' DG I 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" C3' DC I 53 " pdb=" C4' DC I 53 " pdb=" O3' DC I 53 " pdb=" C2' DC I 53 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 2100 not shown) Planarity restraints: 1331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO A 43 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -35 " 0.025 2.00e-02 2.50e+03 1.08e-02 3.51e+00 pdb=" N9 DG I -35 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DG I -35 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I -35 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I -35 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I -35 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I -35 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -26 " 0.022 2.00e-02 2.50e+03 1.09e-02 2.66e+00 pdb=" N1 DC I -26 " -0.020 2.00e-02 2.50e+03 pdb=" C2 DC I -26 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DC I -26 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DC I -26 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I -26 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC I -26 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC I -26 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC I -26 " -0.005 2.00e-02 2.50e+03 ... (remaining 1328 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1131 2.74 - 3.28: 10173 3.28 - 3.82: 24214 3.82 - 4.36: 30965 4.36 - 4.90: 43278 Nonbonded interactions: 109761 Sorted by model distance: nonbonded pdb=" O HIS E 113 " pdb=" O HOH E 201 " model vdw 2.199 3.040 nonbonded pdb=" O HIS B 75 " pdb=" NH2 ARG D 89 " model vdw 2.199 3.120 nonbonded pdb=" NH2 ARG C 32 " pdb=" OE2 GLU D 32 " model vdw 2.204 3.120 nonbonded pdb=" OE2 GLU B 53 " pdb=" O HOH B 201 " model vdw 2.223 3.040 nonbonded pdb=" O LEU B 97 " pdb=" O HOH B 202 " model vdw 2.244 3.040 ... (remaining 109756 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 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and resid 11 through 117) 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: 4.210 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.070 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:5.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 : 0.006 0.041 12749 Z= 0.542 Angle : 0.740 4.983 18461 Z= 0.664 Chirality : 0.044 0.151 2103 Planarity : 0.004 0.052 1331 Dihedral : 28.684 169.163 5506 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.23 % Allowed : 20.06 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.29), residues: 740 helix: 1.92 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.11 (0.33), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 35 TYR 0.012 0.002 TYR D 34 PHE 0.008 0.002 PHE D 67 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.54 (12749) covalent geometry : angle 0.73964 / 0.66 (18461) hydrogen bonds : bond 0.11799 / 7.98 ( 761) hydrogen bonds : angle 3.86455 / 2.76 ( 1906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.340 Fit side-chains REVERT: A 115 LYS cc_start: 0.8048 (mtpm) cc_final: 0.7649 (mtmt) REVERT: A 129 ARG cc_start: 0.7656 (ttt180) cc_final: 0.6741 (tmt170) REVERT: B 91 LYS cc_start: 0.8217 (tttt) cc_final: 0.7794 (ttpt) REVERT: C 36 LYS cc_start: 0.8058 (mttt) cc_final: 0.7765 (mtmt) REVERT: C 61 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7132 (mm-30) REVERT: C 64 GLU cc_start: 0.7289 (tt0) cc_final: 0.7074 (tt0) REVERT: C 95 LYS cc_start: 0.8308 (tppt) cc_final: 0.7979 (tptp) REVERT: C 99 ARG cc_start: 0.8424 (mmt-90) cc_final: 0.7369 (mtp180) REVERT: C 104 GLN cc_start: 0.8645 (mt0) cc_final: 0.7799 (mm110) REVERT: D 109 SER cc_start: 0.8182 (t) cc_final: 0.7751 (m) REVERT: E 56 LYS cc_start: 0.8576 (tttt) cc_final: 0.8128 (ttpp) REVERT: E 59 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7727 (pt0) REVERT: E 76 GLN cc_start: 0.7134 (mt0) cc_final: 0.6655 (pt0) REVERT: E 129 ARG cc_start: 0.7932 (ttt180) cc_final: 0.6643 (tpt90) REVERT: E 131 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.6537 (mtp85) REVERT: F 93 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7737 (mm-40) REVERT: G 95 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7502 (tmtt) REVERT: G 99 ARG cc_start: 0.8107 (mmt180) cc_final: 0.7089 (mmm160) REVERT: G 104 GLN cc_start: 0.8223 (mt0) cc_final: 0.7409 (mm110) REVERT: H 31 LYS cc_start: 0.7955 (tptt) cc_final: 0.7291 (tptm) REVERT: H 113 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7703 (ttmm) outliers start: 14 outliers final: 7 residues processed: 97 average time/residue: 0.7270 time to fit residues: 74.6325 Evaluate side-chains 94 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 88 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.165270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.118911 restraints weight = 10364.899| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 0.67 r_work: 0.3061 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.0500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12749 Z= 0.169 Angle : 0.639 6.746 18461 Z= 0.374 Chirality : 0.046 0.267 2103 Planarity : 0.005 0.054 1331 Dihedral : 31.140 167.740 4032 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.87 % Allowed : 17.99 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.29), residues: 740 helix: 2.14 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.03 (0.34), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 134 TYR 0.011 0.001 TYR B 51 PHE 0.007 0.002 PHE A 67 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (12749) covalent geometry : angle 0.63869 / 0.37 (18461) hydrogen bonds : bond 0.05307 / 3.64 ( 761) hydrogen bonds : angle 3.10552 / 2.23 ( 1906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.292 Fit side-chains REVERT: A 129 ARG cc_start: 0.7860 (ttt180) cc_final: 0.7484 (tmt170) REVERT: C 92 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8259 (mt-10) REVERT: C 99 ARG cc_start: 0.8333 (mmt-90) cc_final: 0.7786 (mtp180) REVERT: C 104 GLN cc_start: 0.8583 (mt0) cc_final: 0.7998 (mm110) REVERT: C 118 LYS cc_start: 0.6837 (OUTLIER) cc_final: 0.5759 (mptt) REVERT: D 102 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: E 56 LYS cc_start: 0.8798 (tttt) cc_final: 0.8536 (ttpp) REVERT: E 76 GLN cc_start: 0.7483 (mt0) cc_final: 0.7242 (pt0) REVERT: E 129 ARG cc_start: 0.7992 (ttt180) cc_final: 0.7359 (tpt90) REVERT: G 95 LYS cc_start: 0.8292 (ttmt) cc_final: 0.8028 (tmtt) REVERT: G 99 ARG cc_start: 0.8179 (mmt180) cc_final: 0.7836 (mmm160) REVERT: G 104 GLN cc_start: 0.8336 (mt0) cc_final: 0.7841 (mm110) REVERT: H 31 LYS cc_start: 0.7947 (tptt) cc_final: 0.7446 (tptm) REVERT: H 113 LYS cc_start: 0.8496 (ttpt) cc_final: 0.8146 (ttmm) outliers start: 18 outliers final: 7 residues processed: 102 average time/residue: 0.7116 time to fit residues: 76.8815 Evaluate side-chains 96 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 98 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 56 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.165652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.121133 restraints weight = 10466.136| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 0.65 r_work: 0.3051 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.0627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12749 Z= 0.146 Angle : 0.615 6.606 18461 Z= 0.363 Chirality : 0.046 0.271 2103 Planarity : 0.004 0.050 1331 Dihedral : 31.109 167.539 4015 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.87 % Allowed : 19.27 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.29), residues: 740 helix: 2.43 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.00 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 78 TYR 0.014 0.001 TYR D 34 PHE 0.008 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.15 (12749) covalent geometry : angle 0.61484 / 0.36 (18461) hydrogen bonds : bond 0.04779 / 3.28 ( 761) hydrogen bonds : angle 2.98594 / 2.14 ( 1906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.336 Fit side-chains REVERT: A 120 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7601 (mtt) REVERT: A 129 ARG cc_start: 0.7895 (ttt180) cc_final: 0.7500 (tmt170) REVERT: B 59 LYS cc_start: 0.8478 (tttm) cc_final: 0.8186 (tttt) REVERT: C 99 ARG cc_start: 0.8325 (mmt-90) cc_final: 0.7812 (mtp180) REVERT: C 104 GLN cc_start: 0.8606 (mt0) cc_final: 0.8013 (mm110) REVERT: C 108 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8621 (mp) REVERT: C 118 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.5731 (mptt) REVERT: D 102 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: E 56 LYS cc_start: 0.8811 (tttt) cc_final: 0.8568 (ttpp) REVERT: E 76 GLN cc_start: 0.7538 (mt0) cc_final: 0.7269 (pt0) REVERT: E 129 ARG cc_start: 0.8001 (ttt180) cc_final: 0.7402 (tpt90) REVERT: G 95 LYS cc_start: 0.8303 (ttmt) cc_final: 0.8046 (tmtt) REVERT: G 99 ARG cc_start: 0.8203 (mmt180) cc_final: 0.7856 (mmm160) REVERT: G 104 GLN cc_start: 0.8365 (mt0) cc_final: 0.7863 (mm110) REVERT: H 31 LYS cc_start: 0.7982 (tptt) cc_final: 0.7493 (tptm) REVERT: H 113 LYS cc_start: 0.8522 (ttpt) cc_final: 0.8183 (ttmm) outliers start: 18 outliers final: 10 residues processed: 99 average time/residue: 0.7161 time to fit residues: 75.1042 Evaluate side-chains 96 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 98 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 chunk 71 optimal weight: 30.0000 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN G 110 ASN H 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.164365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.119764 restraints weight = 10378.482| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 0.64 r_work: 0.3024 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12749 Z= 0.202 Angle : 0.648 7.050 18461 Z= 0.375 Chirality : 0.048 0.281 2103 Planarity : 0.005 0.055 1331 Dihedral : 31.241 166.767 4015 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.71 % Allowed : 19.27 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.29), residues: 740 helix: 2.26 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.15 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 40 TYR 0.015 0.002 TYR D 34 PHE 0.008 0.002 PHE A 67 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.20 (12749) covalent geometry : angle 0.64807 / 0.38 (18461) hydrogen bonds : bond 0.05536 / 3.77 ( 761) hydrogen bonds : angle 2.99374 / 2.15 ( 1906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.313 Fit side-chains REVERT: A 129 ARG cc_start: 0.7878 (ttt180) cc_final: 0.7472 (tmt170) REVERT: B 59 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8149 (tttt) REVERT: C 61 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7325 (mm-30) REVERT: C 99 ARG cc_start: 0.8324 (mmt-90) cc_final: 0.7776 (mtp180) REVERT: C 104 GLN cc_start: 0.8548 (mt0) cc_final: 0.7957 (mm110) REVERT: C 108 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8657 (mp) REVERT: C 118 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.5707 (mptt) REVERT: D 102 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6719 (mp0) REVERT: E 56 LYS cc_start: 0.8805 (tttt) cc_final: 0.8546 (ttpp) REVERT: E 76 GLN cc_start: 0.7484 (mt0) cc_final: 0.7219 (pt0) REVERT: E 129 ARG cc_start: 0.7983 (ttt180) cc_final: 0.7357 (tpt90) REVERT: G 95 LYS cc_start: 0.8271 (ttmt) cc_final: 0.8016 (tmtt) REVERT: G 99 ARG cc_start: 0.8176 (mmt180) cc_final: 0.7817 (mmm160) REVERT: G 104 GLN cc_start: 0.8359 (mt0) cc_final: 0.7843 (mm110) REVERT: H 31 LYS cc_start: 0.8000 (tptt) cc_final: 0.7487 (tptm) REVERT: H 113 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8151 (ttmm) outliers start: 17 outliers final: 9 residues processed: 97 average time/residue: 0.7202 time to fit residues: 73.7107 Evaluate side-chains 95 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN H 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.164022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.117299 restraints weight = 10447.238| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 0.67 r_work: 0.3044 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12749 Z= 0.150 Angle : 0.627 6.856 18461 Z= 0.367 Chirality : 0.046 0.277 2103 Planarity : 0.004 0.053 1331 Dihedral : 31.237 166.715 4015 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.14 % Allowed : 17.99 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.29), residues: 740 helix: 2.30 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.13 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 35 TYR 0.013 0.001 TYR B 51 PHE 0.010 0.001 PHE A 67 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.15 (12749) covalent geometry : angle 0.62700 / 0.37 (18461) hydrogen bonds : bond 0.05162 / 3.53 ( 761) hydrogen bonds : angle 2.97777 / 2.14 ( 1906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.193 Fit side-chains REVERT: A 120 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7583 (mtt) REVERT: A 129 ARG cc_start: 0.7867 (ttt180) cc_final: 0.7467 (tmt170) REVERT: B 59 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8134 (tttt) REVERT: C 61 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7296 (mm-30) REVERT: C 99 ARG cc_start: 0.8323 (mmt-90) cc_final: 0.7787 (mtp180) REVERT: C 104 GLN cc_start: 0.8551 (mt0) cc_final: 0.7951 (mm110) REVERT: C 108 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8654 (mp) REVERT: C 118 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.5715 (mptt) REVERT: D 102 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: E 56 LYS cc_start: 0.8781 (tttt) cc_final: 0.8534 (ttpp) REVERT: E 76 GLN cc_start: 0.7486 (mt0) cc_final: 0.7221 (pt0) REVERT: E 129 ARG cc_start: 0.7960 (ttt180) cc_final: 0.7355 (tpt90) REVERT: E 131 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.6631 (mtp85) REVERT: F 92 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7671 (mtp85) REVERT: G 51 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8002 (tp) REVERT: G 95 LYS cc_start: 0.8277 (ttmt) cc_final: 0.8026 (tmtt) REVERT: G 99 ARG cc_start: 0.8193 (mmt180) cc_final: 0.7831 (mmm160) REVERT: G 104 GLN cc_start: 0.8368 (mt0) cc_final: 0.7859 (mm110) REVERT: H 31 LYS cc_start: 0.7976 (tptt) cc_final: 0.7501 (tptm) REVERT: H 113 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8165 (ttmm) outliers start: 26 outliers final: 11 residues processed: 104 average time/residue: 0.7313 time to fit residues: 80.2499 Evaluate side-chains 102 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 64 optimal weight: 0.0970 chunk 53 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.165482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.121506 restraints weight = 10319.309| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 0.63 r_work: 0.3029 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12749 Z= 0.147 Angle : 0.625 6.948 18461 Z= 0.365 Chirality : 0.046 0.276 2103 Planarity : 0.004 0.052 1331 Dihedral : 31.236 166.767 4015 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.50 % Allowed : 18.79 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.29), residues: 740 helix: 2.41 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.11 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 35 TYR 0.012 0.001 TYR B 51 PHE 0.009 0.001 PHE A 67 HIS 0.007 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (12749) covalent geometry : angle 0.62536 / 0.36 (18461) hydrogen bonds : bond 0.05013 / 3.43 ( 761) hydrogen bonds : angle 2.96376 / 2.13 ( 1906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.228 Fit side-chains REVERT: A 129 ARG cc_start: 0.7903 (ttt180) cc_final: 0.7503 (tmt170) REVERT: B 59 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8169 (tttt) REVERT: C 61 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7317 (mm-30) REVERT: C 99 ARG cc_start: 0.8353 (mmt-90) cc_final: 0.7830 (mtp180) REVERT: C 104 GLN cc_start: 0.8584 (mt0) cc_final: 0.7993 (mm110) REVERT: C 108 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8658 (mp) REVERT: C 118 LYS cc_start: 0.6800 (OUTLIER) cc_final: 0.5719 (mptt) REVERT: D 102 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: E 56 LYS cc_start: 0.8797 (tttt) cc_final: 0.8555 (ttpp) REVERT: E 76 GLN cc_start: 0.7520 (mt0) cc_final: 0.7261 (pt0) REVERT: E 120 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7989 (mtt) REVERT: E 129 ARG cc_start: 0.8004 (ttt180) cc_final: 0.7377 (tpt90) REVERT: F 92 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7683 (mtp85) REVERT: G 51 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8006 (tp) REVERT: G 95 LYS cc_start: 0.8290 (ttmt) cc_final: 0.8046 (tmtt) REVERT: G 99 ARG cc_start: 0.8220 (mmt180) cc_final: 0.7854 (mmm160) REVERT: G 104 GLN cc_start: 0.8396 (mt0) cc_final: 0.7893 (mm110) REVERT: H 31 LYS cc_start: 0.7995 (tptt) cc_final: 0.7526 (tptm) REVERT: H 113 LYS cc_start: 0.8533 (ttpt) cc_final: 0.8189 (ttmm) outliers start: 22 outliers final: 12 residues processed: 98 average time/residue: 0.7249 time to fit residues: 75.0462 Evaluate side-chains 103 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 88 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 71 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.164538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.118025 restraints weight = 10339.300| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 0.67 r_work: 0.3049 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12749 Z= 0.176 Angle : 0.633 6.961 18461 Z= 0.367 Chirality : 0.047 0.276 2103 Planarity : 0.004 0.053 1331 Dihedral : 31.240 167.118 4015 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.18 % Allowed : 19.27 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.29), residues: 740 helix: 2.38 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.12 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 78 TYR 0.011 0.001 TYR D 34 PHE 0.008 0.002 PHE A 67 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 (12749) covalent geometry : angle 0.63284 / 0.37 (18461) hydrogen bonds : bond 0.05155 / 3.52 ( 761) hydrogen bonds : angle 2.95602 / 2.12 ( 1906) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.231 Fit side-chains REVERT: A 129 ARG cc_start: 0.7871 (ttt180) cc_final: 0.7473 (tmt170) REVERT: B 59 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8160 (tttt) REVERT: C 99 ARG cc_start: 0.8332 (mmt-90) cc_final: 0.7805 (mtp180) REVERT: C 104 GLN cc_start: 0.8561 (mt0) cc_final: 0.7960 (mm110) REVERT: C 108 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8662 (mp) REVERT: C 118 LYS cc_start: 0.6783 (OUTLIER) cc_final: 0.5707 (mptt) REVERT: D 102 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: E 56 LYS cc_start: 0.8794 (tttt) cc_final: 0.8539 (ttpp) REVERT: E 76 GLN cc_start: 0.7477 (mt0) cc_final: 0.7207 (pt0) REVERT: E 129 ARG cc_start: 0.7974 (ttt180) cc_final: 0.7364 (tpt90) REVERT: F 92 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7687 (mtp85) REVERT: G 51 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8018 (tp) REVERT: G 95 LYS cc_start: 0.8269 (ttmt) cc_final: 0.8016 (tmtt) REVERT: G 99 ARG cc_start: 0.8191 (mmt180) cc_final: 0.7806 (mmm160) REVERT: G 104 GLN cc_start: 0.8376 (mt0) cc_final: 0.7871 (mm110) REVERT: H 31 LYS cc_start: 0.7975 (tptt) cc_final: 0.7498 (tptm) REVERT: H 113 LYS cc_start: 0.8504 (ttpt) cc_final: 0.8151 (ttmm) outliers start: 20 outliers final: 12 residues processed: 99 average time/residue: 0.7548 time to fit residues: 79.0262 Evaluate side-chains 100 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.166051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.119437 restraints weight = 10334.125| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 0.67 r_work: 0.3121 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12749 Z= 0.141 Angle : 0.616 6.742 18461 Z= 0.361 Chirality : 0.045 0.273 2103 Planarity : 0.004 0.051 1331 Dihedral : 31.222 166.928 4015 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.34 % Allowed : 19.11 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.29), residues: 740 helix: 2.45 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.07 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 78 TYR 0.011 0.001 TYR B 51 PHE 0.009 0.001 PHE A 67 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (12749) covalent geometry : angle 0.61611 / 0.36 (18461) hydrogen bonds : bond 0.04820 / 3.30 ( 761) hydrogen bonds : angle 2.95018 / 2.12 ( 1906) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.263 Fit side-chains REVERT: A 129 ARG cc_start: 0.7748 (ttt180) cc_final: 0.7316 (tmt170) REVERT: B 59 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8063 (tttt) REVERT: C 99 ARG cc_start: 0.8326 (mmt-90) cc_final: 0.7707 (mtp180) REVERT: C 104 GLN cc_start: 0.8576 (mt0) cc_final: 0.7910 (mm110) REVERT: C 108 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8642 (mp) REVERT: C 118 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.5710 (mptt) REVERT: D 102 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6618 (mp0) REVERT: E 56 LYS cc_start: 0.8754 (tttt) cc_final: 0.8465 (ttpp) REVERT: E 76 GLN cc_start: 0.7357 (mt0) cc_final: 0.7071 (pt0) REVERT: E 120 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7897 (mtt) REVERT: E 129 ARG cc_start: 0.7915 (ttt180) cc_final: 0.7244 (tpt90) REVERT: F 92 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7602 (mtp85) REVERT: G 51 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8013 (tp) REVERT: G 95 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7901 (tmtt) REVERT: G 99 ARG cc_start: 0.8148 (mmt180) cc_final: 0.7709 (mmm160) REVERT: G 104 GLN cc_start: 0.8311 (mt0) cc_final: 0.7755 (mm110) REVERT: H 31 LYS cc_start: 0.7908 (tptt) cc_final: 0.7386 (tptm) REVERT: H 113 LYS cc_start: 0.8452 (ttpt) cc_final: 0.8075 (ttmm) outliers start: 21 outliers final: 13 residues processed: 99 average time/residue: 0.7374 time to fit residues: 77.2984 Evaluate side-chains 102 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 88 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 68 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 88 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.163120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.117156 restraints weight = 10241.123| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 0.64 r_work: 0.3013 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12749 Z= 0.238 Angle : 0.681 7.273 18461 Z= 0.387 Chirality : 0.050 0.280 2103 Planarity : 0.005 0.055 1331 Dihedral : 31.363 166.832 4015 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.71 % Allowed : 19.43 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.29), residues: 740 helix: 2.12 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.25 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 42 TYR 0.017 0.002 TYR A 54 PHE 0.009 0.002 PHE D 67 HIS 0.007 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.24 (12749) covalent geometry : angle 0.68110 / 0.39 (18461) hydrogen bonds : bond 0.05932 / 4.03 ( 761) hydrogen bonds : angle 3.04291 / 2.19 ( 1906) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.322 Fit side-chains REVERT: A 129 ARG cc_start: 0.7842 (ttt180) cc_final: 0.7439 (tmt170) REVERT: B 59 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8118 (tttt) REVERT: C 99 ARG cc_start: 0.8338 (mmt-90) cc_final: 0.7777 (mtp180) REVERT: C 108 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8705 (mp) REVERT: C 118 LYS cc_start: 0.6802 (OUTLIER) cc_final: 0.5700 (mptt) REVERT: D 102 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6764 (mp0) REVERT: E 56 LYS cc_start: 0.8788 (tttt) cc_final: 0.8525 (ttpp) REVERT: E 76 GLN cc_start: 0.7451 (mt0) cc_final: 0.7212 (pt0) REVERT: E 129 ARG cc_start: 0.7994 (ttt180) cc_final: 0.7351 (tpt90) REVERT: G 51 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8052 (tp) REVERT: G 95 LYS cc_start: 0.8246 (ttmt) cc_final: 0.8004 (tmtt) REVERT: G 99 ARG cc_start: 0.8168 (mmt180) cc_final: 0.7828 (mmm160) REVERT: G 104 GLN cc_start: 0.8352 (mt0) cc_final: 0.7842 (mm110) REVERT: H 31 LYS cc_start: 0.7978 (tptt) cc_final: 0.7496 (tptm) REVERT: H 113 LYS cc_start: 0.8502 (ttpt) cc_final: 0.8218 (ttmm) outliers start: 17 outliers final: 12 residues processed: 94 average time/residue: 0.7244 time to fit residues: 72.2230 Evaluate side-chains 96 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 71 optimal weight: 30.0000 chunk 80 optimal weight: 9.9990 chunk 1 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.165105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.118379 restraints weight = 10239.280| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 0.67 r_work: 0.3024 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12749 Z= 0.145 Angle : 0.642 7.077 18461 Z= 0.371 Chirality : 0.047 0.274 2103 Planarity : 0.005 0.060 1331 Dihedral : 31.335 166.647 4015 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.87 % Allowed : 19.11 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.29), residues: 740 helix: 2.30 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.18 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 78 TYR 0.015 0.002 TYR A 54 PHE 0.008 0.002 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.15 (12749) covalent geometry : angle 0.64221 / 0.37 (18461) hydrogen bonds : bond 0.05035 / 3.44 ( 761) hydrogen bonds : angle 3.02431 / 2.17 ( 1906) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.210 Fit side-chains REVERT: A 129 ARG cc_start: 0.7799 (ttt180) cc_final: 0.7366 (tmt170) REVERT: B 59 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8093 (tttt) REVERT: C 99 ARG cc_start: 0.8319 (mmt-90) cc_final: 0.7761 (mtp180) REVERT: C 104 GLN cc_start: 0.8589 (mt0) cc_final: 0.7963 (mm110) REVERT: C 108 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8645 (mp) REVERT: C 118 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.5671 (mptt) REVERT: D 102 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6697 (mp0) REVERT: E 56 LYS cc_start: 0.8764 (tttt) cc_final: 0.8500 (ttpp) REVERT: E 76 GLN cc_start: 0.7451 (mt0) cc_final: 0.7171 (pt0) REVERT: E 129 ARG cc_start: 0.7948 (ttt180) cc_final: 0.7296 (tpt90) REVERT: G 51 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.7983 (tp) REVERT: G 95 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7980 (tmtt) REVERT: G 99 ARG cc_start: 0.8170 (mmt180) cc_final: 0.7801 (mmm160) REVERT: G 104 GLN cc_start: 0.8339 (mt0) cc_final: 0.7821 (mm110) REVERT: H 31 LYS cc_start: 0.7949 (tptt) cc_final: 0.7453 (tptm) REVERT: H 113 LYS cc_start: 0.8480 (ttpt) cc_final: 0.8130 (ttmm) outliers start: 18 outliers final: 12 residues processed: 99 average time/residue: 0.6843 time to fit residues: 71.8620 Evaluate side-chains 99 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 97 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 53 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.164819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.118125 restraints weight = 10237.088| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 0.67 r_work: 0.3061 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12749 Z= 0.163 Angle : 0.645 7.251 18461 Z= 0.370 Chirality : 0.047 0.278 2103 Planarity : 0.004 0.062 1331 Dihedral : 31.339 167.287 4015 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.71 % Allowed : 19.11 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.29), residues: 740 helix: 2.34 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.17 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 78 TYR 0.014 0.002 TYR A 54 PHE 0.008 0.001 PHE A 67 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (12749) covalent geometry : angle 0.64533 / 0.37 (18461) hydrogen bonds : bond 0.05124 / 3.50 ( 761) hydrogen bonds : angle 2.98160 / 2.14 ( 1906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3164.17 seconds wall clock time: 54 minutes 26.96 seconds (3266.96 seconds total)