Starting phenix.real_space_refine on Fri Jul 3 14:07:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9si3_54924/07_2026/9si3_54924.cif Found real_map, /net/cci-nas-00/data/ceres_data/9si3_54924/07_2026/9si3_54924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9si3_54924/07_2026/9si3_54924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9si3_54924/07_2026/9si3_54924.map" model { file = "/net/cci-nas-00/data/ceres_data/9si3_54924/07_2026/9si3_54924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9si3_54924/07_2026/9si3_54924.cif" } resolution = 2.83 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= 0.029 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 293 5.49 5 S 26 5.16 5 C 8146 2.51 5 N 2686 2.21 5 O 3250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14401 Number of models: 1 Model: "" Number of chains: 14 Chain: "L" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 108 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" 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: "C" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 831 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 871 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3034 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2990 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "O" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 633 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "M" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1118 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 9, 'TRANS': 127} Chain: "N" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 346 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Time building chain proxies: 2.95, per 1000 atoms: 0.20 Number of scatterers: 14401 At special positions: 0 Unit cell: (100.326, 148.308, 118.501, 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 26 16.00 P 293 15.00 O 3250 8.00 N 2686 7.00 C 8146 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 465.4 milliseconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1976 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 71.8% alpha, 2.2% beta 147 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'L' and resid 9 through 17 Processing helix chain 'A' and resid 44 through 57 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 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.821A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.530A 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 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 4.042A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.987A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.588A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.795A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.599A 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 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.619A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.568A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 4.261A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 61 removed outlier: 3.613A pdb=" N LEU O 61 " --> pdb=" O GLU O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 67 Processing helix chain 'O' and resid 69 through 76 removed outlier: 3.611A pdb=" N TYR O 73 " --> pdb=" O ASN O 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 13 Processing helix chain 'M' and resid 14 through 21 removed outlier: 4.013A pdb=" N THR M 21 " --> pdb=" O HIS M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 42 Processing helix chain 'M' and resid 72 through 81 Processing helix chain 'M' and resid 85 through 89 removed outlier: 3.685A pdb=" N VAL M 89 " --> pdb=" O PHE M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 92 through 96 Processing helix chain 'M' and resid 97 through 141 removed outlier: 3.559A pdb=" N MET M 141 " --> pdb=" O GLN M 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 46 removed outlier: 4.606A pdb=" N GLU N 13 " --> pdb=" O ILE N 9 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU N 31 " --> pdb=" O ASP N 27 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL N 32 " --> pdb=" O ASN N 28 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.189A 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 'C' and resid 42 through 43 removed outlier: 7.495A 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 100 through 102 removed outlier: 6.820A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.120A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.465A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'M' and resid 43 through 45 551 hydrogen bonds defined for protein. 1617 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 377 hydrogen bonds 754 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1964 1.32 - 1.45: 5349 1.45 - 1.57: 7316 1.57 - 1.69: 585 1.69 - 1.82: 42 Bond restraints: 15256 Sorted by residual: bond pdb=" CA SER O 15 " pdb=" CB SER O 15 " ideal model delta sigma weight residual 1.531 1.482 0.048 1.59e-02 3.96e+03 9.28e+00 bond pdb=" C3' DC I 33 " pdb=" C2' DC I 33 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.72e+00 bond pdb=" C3' DT J 235 " pdb=" C2' DT J 235 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.58e+00 bond pdb=" C3' DA J 198 " pdb=" C2' DA J 198 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.30e+00 bond pdb=" C3' DA J 285 " pdb=" C2' DA J 285 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.09e+00 ... (remaining 15251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 21382 2.31 - 4.63: 418 4.63 - 6.94: 25 6.94 - 9.26: 3 9.26 - 11.57: 4 Bond angle restraints: 21832 Sorted by residual: angle pdb=" O4' DC J 289 " pdb=" C4' DC J 289 " pdb=" C3' DC J 289 " ideal model delta sigma weight residual 106.00 102.91 3.09 6.00e-01 2.78e+00 2.65e+01 angle pdb=" O4' DG I 130 " pdb=" C4' DG I 130 " pdb=" C3' DG I 130 " ideal model delta sigma weight residual 106.00 103.19 2.81 6.00e-01 2.78e+00 2.19e+01 angle pdb=" N3 DT J 178 " pdb=" C4 DT J 178 " pdb=" O4 DT J 178 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.06e+01 angle pdb=" N3 DT I 6 " pdb=" C4 DT I 6 " pdb=" O4 DT I 6 " 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 J 221 " pdb=" C4 DT J 221 " pdb=" O4 DT J 221 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 ... (remaining 21827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.20: 5991 21.20 - 42.40: 1378 42.40 - 63.60: 1085 63.60 - 84.80: 34 84.80 - 106.00: 2 Dihedral angle restraints: 8490 sinusoidal: 5449 harmonic: 3041 Sorted by residual: dihedral pdb=" CG ARG E 83 " pdb=" CD ARG E 83 " pdb=" NE ARG E 83 " pdb=" CZ ARG E 83 " ideal model delta sinusoidal sigma weight residual 90.00 41.11 48.89 2 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" C4' DA J 151 " pdb=" C3' DA J 151 " pdb=" O3' DA J 151 " pdb=" P DG J 152 " ideal model delta sinusoidal sigma weight residual -140.00 -34.00 -106.00 1 3.50e+01 8.16e-04 1.00e+01 dihedral pdb=" CG ARG B 67 " pdb=" CD ARG B 67 " pdb=" NE ARG B 67 " pdb=" CZ ARG B 67 " ideal model delta sinusoidal sigma weight residual 90.00 47.30 42.70 2 1.50e+01 4.44e-03 9.81e+00 ... (remaining 8487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1449 0.031 - 0.061: 639 0.061 - 0.092: 245 0.092 - 0.122: 111 0.122 - 0.153: 17 Chirality restraints: 2461 Sorted by residual: chirality pdb=" C3' DG I 52 " pdb=" C4' DG I 52 " pdb=" O3' DG I 52 " pdb=" C2' DG I 52 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" C3' DT I 34 " pdb=" C4' DT I 34 " pdb=" O3' DT I 34 " pdb=" C2' DT I 34 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" C3' DC J 241 " pdb=" C4' DC J 241 " pdb=" O3' DC J 241 " pdb=" C2' DC J 241 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 2458 not shown) Planarity restraints: 1752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA O 11 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.05e+00 pdb=" C ALA O 11 " 0.043 2.00e-02 2.50e+03 pdb=" O ALA O 11 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS O 12 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA N 5 " -0.033 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO N 6 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO N 6 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO N 6 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU M 125 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" CD GLU M 125 " -0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU M 125 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU M 125 " 0.012 2.00e-02 2.50e+03 ... (remaining 1749 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1941 2.76 - 3.29: 12907 3.29 - 3.83: 28057 3.83 - 4.36: 32444 4.36 - 4.90: 47495 Nonbonded interactions: 122844 Sorted by model distance: nonbonded pdb=" NH1 ARG L 9 " pdb=" OE1 GLU C 92 " model vdw 2.222 3.120 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.350 3.040 nonbonded pdb=" O ALA M 114 " pdb=" OD1 ASN M 118 " model vdw 2.382 3.040 nonbonded pdb=" OG1 THR A 118 " pdb=" CD ARG B 45 " model vdw 2.515 3.440 nonbonded pdb=" O ASN O 14 " pdb=" C SER O 15 " model vdw 2.528 3.270 ... (remaining 122839 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' selection = (chain 'E' and resid 37 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 9 through 120) } 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=0.00 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: 5.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.740 Find NCS groups from input model: 0.120 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:7.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 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 0.048 15256 Z= 0.493 Angle : 0.743 11.572 21832 Z= 0.640 Chirality : 0.043 0.153 2461 Planarity : 0.004 0.051 1752 Dihedral : 26.816 106.002 6514 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 16.82 % Favored : 83.18 % 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: 2.38 (0.26), residues: 1021 helix: 2.52 (0.19), residues: 713 sheet: -2.51 (1.81), residues: 10 loop : -0.68 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 83 TYR 0.009 0.001 TYR D 40 PHE 0.008 0.001 PHE E 67 TRP 0.029 0.002 TRP M 25 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.49 (15256) covalent geometry : angle 0.74259 / 0.64 (21832) hydrogen bonds : bond 0.10512 / 6.94 ( 928) hydrogen bonds : angle 3.61792 / 2.72 ( 2371) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 105 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8208 (mm-30) REVERT: H 42 TYR cc_start: 0.8499 (t80) cc_final: 0.8205 (t80) outliers start: 0 outliers final: 1 residues processed: 310 average time/residue: 0.7723 time to fit residues: 256.0137 Evaluate side-chains 244 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 87 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 0.0370 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.1840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 68 GLN A 113 HIS C 24 GLN F 75 HIS N 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.083835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.052249 restraints weight = 41989.428| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.71 r_work: 0.2667 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15256 Z= 0.167 Angle : 0.664 12.889 21832 Z= 0.379 Chirality : 0.043 0.367 2461 Planarity : 0.005 0.047 1752 Dihedral : 30.284 105.890 4364 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.29 % Allowed : 22.46 % Favored : 73.25 % 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: 2.44 (0.26), residues: 1021 helix: 2.51 (0.19), residues: 722 sheet: -2.73 (1.68), residues: 10 loop : -0.60 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 29 TYR 0.011 0.001 TYR D 40 PHE 0.011 0.001 PHE N 45 TRP 0.014 0.002 TRP M 25 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.17 (15256) covalent geometry : angle 0.66439 / 0.38 (21832) hydrogen bonds : bond 0.04661 / 3.01 ( 928) hydrogen bonds : angle 3.18640 / 2.34 ( 2371) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 245 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8807 (ptp-110) REVERT: A 56 LYS cc_start: 0.9402 (ttpp) cc_final: 0.9149 (ttmm) REVERT: A 59 GLU cc_start: 0.8255 (pm20) cc_final: 0.7908 (pm20) REVERT: A 73 GLU cc_start: 0.8958 (tt0) cc_final: 0.8408 (tt0) REVERT: B 25 ASN cc_start: 0.8971 (m110) cc_final: 0.8362 (m110) REVERT: D 34 LYS cc_start: 0.9168 (mmmm) cc_final: 0.8880 (mppt) REVERT: D 35 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8217 (mm-30) REVERT: D 68 ASP cc_start: 0.9129 (t0) cc_final: 0.8905 (t0) REVERT: D 105 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8547 (mt-10) REVERT: E 99 TYR cc_start: 0.9409 (t80) cc_final: 0.9193 (t80) REVERT: F 59 LYS cc_start: 0.9268 (tttm) cc_final: 0.9064 (tppp) REVERT: F 77 LYS cc_start: 0.9525 (OUTLIER) cc_final: 0.9239 (mtpt) REVERT: G 20 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8747 (mtt-85) REVERT: G 92 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8185 (mt-10) REVERT: H 33 ARG cc_start: 0.8134 (ttm110) cc_final: 0.7407 (mtp-110) REVERT: H 35 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8033 (mt-10) REVERT: H 42 TYR cc_start: 0.8528 (t80) cc_final: 0.8186 (t80) REVERT: H 93 GLU cc_start: 0.9113 (mp0) cc_final: 0.8459 (mp0) REVERT: H 105 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8613 (mt-10) REVERT: O 12 LYS cc_start: 0.9153 (ttmt) cc_final: 0.8903 (mtpt) REVERT: O 35 ARG cc_start: 0.8941 (mmm160) cc_final: 0.8481 (mtm-85) REVERT: N 44 MET cc_start: 0.8900 (mmt) cc_final: 0.8617 (mmt) outliers start: 38 outliers final: 10 residues processed: 263 average time/residue: 0.7817 time to fit residues: 219.9939 Evaluate side-chains 250 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 237 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 33 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 70 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 118 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 89 optimal weight: 30.0000 chunk 41 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN F 27 GLN O 44 GLN M 118 ASN N 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.083755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.051721 restraints weight = 42333.969| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.70 r_work: 0.2657 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15256 Z= 0.163 Angle : 0.643 12.090 21832 Z= 0.366 Chirality : 0.042 0.344 2461 Planarity : 0.005 0.044 1752 Dihedral : 30.404 104.814 4362 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.39 % Allowed : 23.25 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.50 (0.26), residues: 1021 helix: 2.58 (0.19), residues: 722 sheet: -2.89 (1.66), residues: 10 loop : -0.64 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 132 TYR 0.011 0.001 TYR D 40 PHE 0.011 0.001 PHE M 22 TRP 0.011 0.002 TRP M 25 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (15256) covalent geometry : angle 0.64317 / 0.37 (21832) hydrogen bonds : bond 0.04397 / 2.86 ( 928) hydrogen bonds : angle 3.10118 / 2.28 ( 2371) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8813 (ptp-110) REVERT: A 56 LYS cc_start: 0.9394 (ttpp) cc_final: 0.9153 (ttmm) REVERT: A 59 GLU cc_start: 0.8281 (pm20) cc_final: 0.7914 (pm20) REVERT: D 35 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8181 (mm-30) REVERT: D 42 TYR cc_start: 0.8662 (t80) cc_final: 0.8265 (t80) REVERT: D 105 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8497 (mt-10) REVERT: F 77 LYS cc_start: 0.9522 (OUTLIER) cc_final: 0.9247 (mtpt) REVERT: G 15 LYS cc_start: 0.9144 (ttmm) cc_final: 0.8812 (ttpp) REVERT: G 92 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8113 (mt-10) REVERT: H 42 TYR cc_start: 0.8500 (t80) cc_final: 0.8168 (t80) REVERT: H 93 GLU cc_start: 0.9160 (mp0) cc_final: 0.8937 (mp0) REVERT: H 105 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8562 (mt-10) REVERT: O 12 LYS cc_start: 0.9173 (ttmt) cc_final: 0.8859 (mtpt) REVERT: O 17 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8293 (ttt180) REVERT: O 20 LYS cc_start: 0.9203 (pptt) cc_final: 0.8925 (pptt) REVERT: M 91 LYS cc_start: 0.6897 (OUTLIER) cc_final: 0.6562 (pptt) REVERT: M 118 ASN cc_start: 0.9391 (OUTLIER) cc_final: 0.9109 (p0) REVERT: N 44 MET cc_start: 0.8963 (mmt) cc_final: 0.8457 (mmt) outliers start: 30 outliers final: 12 residues processed: 252 average time/residue: 0.7604 time to fit residues: 205.6575 Evaluate side-chains 245 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 228 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain O residue 17 ARG Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain M residue 91 LYS Chi-restraints excluded: chain M residue 118 ASN Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 30 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 67 optimal weight: 0.0870 chunk 126 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 120 optimal weight: 30.0000 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN N 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.083396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.051498 restraints weight = 42582.651| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.73 r_work: 0.2658 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15256 Z= 0.168 Angle : 0.648 11.766 21832 Z= 0.363 Chirality : 0.042 0.362 2461 Planarity : 0.005 0.064 1752 Dihedral : 30.500 104.443 4362 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.27 % Allowed : 22.91 % Favored : 73.81 % 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: 2.51 (0.26), residues: 1021 helix: 2.59 (0.19), residues: 725 sheet: -3.02 (1.64), residues: 10 loop : -0.66 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 30 TYR 0.012 0.001 TYR D 40 PHE 0.017 0.001 PHE M 124 TRP 0.009 0.002 TRP M 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.17 (15256) covalent geometry : angle 0.64847 / 0.36 (21832) hydrogen bonds : bond 0.04275 / 2.77 ( 928) hydrogen bonds : angle 3.12067 / 2.29 ( 2371) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 238 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8965 (ptp-110) REVERT: A 56 LYS cc_start: 0.9432 (ttpp) cc_final: 0.9209 (ttmm) REVERT: A 59 GLU cc_start: 0.8371 (pm20) cc_final: 0.8056 (pm20) REVERT: D 35 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8223 (mm-30) REVERT: D 42 TYR cc_start: 0.8779 (t80) cc_final: 0.8392 (t80) REVERT: D 105 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8565 (mt-10) REVERT: E 59 GLU cc_start: 0.8833 (pm20) cc_final: 0.8494 (pm20) REVERT: E 129 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8122 (tmm160) REVERT: F 77 LYS cc_start: 0.9479 (OUTLIER) cc_final: 0.9246 (mtpt) REVERT: G 15 LYS cc_start: 0.9290 (ttmm) cc_final: 0.8998 (ttpp) REVERT: G 92 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8192 (mt-10) REVERT: H 33 ARG cc_start: 0.8202 (ttm110) cc_final: 0.7527 (mtp-110) REVERT: H 35 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8046 (mt-10) REVERT: H 42 TYR cc_start: 0.8684 (t80) cc_final: 0.8343 (t80) REVERT: O 12 LYS cc_start: 0.9268 (ttmt) cc_final: 0.8986 (mtpt) REVERT: O 40 GLU cc_start: 0.9595 (tp30) cc_final: 0.9310 (tp30) REVERT: M 91 LYS cc_start: 0.6887 (OUTLIER) cc_final: 0.6585 (pptt) REVERT: N 44 MET cc_start: 0.8982 (mmt) cc_final: 0.8548 (mmt) outliers start: 29 outliers final: 8 residues processed: 252 average time/residue: 0.7700 time to fit residues: 207.3369 Evaluate side-chains 237 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 225 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain M residue 91 LYS Chi-restraints excluded: chain M residue 124 PHE Chi-restraints excluded: chain N residue 16 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN F 27 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN G 112 GLN O 44 GLN ** M 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.083865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.052021 restraints weight = 42492.756| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.73 r_work: 0.2672 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15256 Z= 0.148 Angle : 0.640 11.520 21832 Z= 0.361 Chirality : 0.041 0.370 2461 Planarity : 0.004 0.041 1752 Dihedral : 30.512 103.860 4362 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.71 % Allowed : 24.15 % Favored : 73.14 % 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: 2.54 (0.26), residues: 1021 helix: 2.60 (0.19), residues: 725 sheet: -3.21 (1.61), residues: 10 loop : -0.62 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 132 TYR 0.011 0.001 TYR D 40 PHE 0.015 0.001 PHE M 58 TRP 0.008 0.001 TRP M 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (15256) covalent geometry : angle 0.64016 / 0.36 (21832) hydrogen bonds : bond 0.04089 / 2.67 ( 928) hydrogen bonds : angle 3.05300 / 2.24 ( 2371) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8973 (ptp-110) REVERT: A 56 LYS cc_start: 0.9437 (ttpp) cc_final: 0.9219 (ttmm) REVERT: A 59 GLU cc_start: 0.8362 (pm20) cc_final: 0.8033 (pm20) REVERT: D 35 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8266 (mm-30) REVERT: D 42 TYR cc_start: 0.8756 (t80) cc_final: 0.8392 (t80) REVERT: D 105 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8544 (mt-10) REVERT: E 59 GLU cc_start: 0.8861 (pm20) cc_final: 0.8486 (pm20) REVERT: E 129 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8119 (tmm160) REVERT: G 15 LYS cc_start: 0.9266 (ttmm) cc_final: 0.8971 (ttpp) REVERT: G 92 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8274 (mt-10) REVERT: H 33 ARG cc_start: 0.8178 (ttm110) cc_final: 0.7492 (mtp-110) REVERT: H 35 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8031 (mt-10) REVERT: H 42 TYR cc_start: 0.8666 (t80) cc_final: 0.8324 (t80) REVERT: O 12 LYS cc_start: 0.9253 (ttmt) cc_final: 0.9025 (mtpt) REVERT: O 40 GLU cc_start: 0.9675 (tp30) cc_final: 0.9202 (tp30) REVERT: O 44 GLN cc_start: 0.9217 (mm-40) cc_final: 0.8892 (mm-40) REVERT: M 91 LYS cc_start: 0.6938 (pttp) cc_final: 0.6660 (pptt) REVERT: M 120 LYS cc_start: 0.9511 (ptpt) cc_final: 0.9096 (pttt) REVERT: N 44 MET cc_start: 0.8961 (mmt) cc_final: 0.8481 (mmt) outliers start: 24 outliers final: 11 residues processed: 250 average time/residue: 0.8156 time to fit residues: 218.1112 Evaluate side-chains 242 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 229 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain M residue 124 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 34 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 94 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN M 11 GLN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.083118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.051166 restraints weight = 42635.525| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.70 r_work: 0.2650 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 15256 Z= 0.192 Angle : 0.668 12.672 21832 Z= 0.371 Chirality : 0.042 0.383 2461 Planarity : 0.005 0.049 1752 Dihedral : 30.592 103.550 4362 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.93 % Allowed : 24.27 % Favored : 72.80 % 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: 2.51 (0.26), residues: 1021 helix: 2.58 (0.19), residues: 725 sheet: -3.20 (1.60), residues: 10 loop : -0.65 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 132 TYR 0.010 0.001 TYR D 40 PHE 0.010 0.001 PHE N 45 TRP 0.006 0.001 TRP M 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.19 (15256) covalent geometry : angle 0.66766 / 0.37 (21832) hydrogen bonds : bond 0.04314 / 2.81 ( 928) hydrogen bonds : angle 3.11056 / 2.28 ( 2371) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.8951 (ptp-110) REVERT: A 56 LYS cc_start: 0.9443 (ttpp) cc_final: 0.9232 (ttmm) REVERT: A 59 GLU cc_start: 0.8411 (pm20) cc_final: 0.8080 (pm20) REVERT: A 106 ASP cc_start: 0.9312 (m-30) cc_final: 0.8913 (m-30) REVERT: D 35 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8259 (mm-30) REVERT: D 42 TYR cc_start: 0.8810 (t80) cc_final: 0.8470 (t80) REVERT: E 59 GLU cc_start: 0.8905 (pm20) cc_final: 0.8525 (pm20) REVERT: E 129 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8170 (tmm160) REVERT: F 93 GLN cc_start: 0.9150 (mm-40) cc_final: 0.8879 (mm110) REVERT: G 15 LYS cc_start: 0.9267 (ttmm) cc_final: 0.8955 (ttpp) REVERT: G 92 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8334 (mt-10) REVERT: H 35 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8048 (mt-10) REVERT: H 42 TYR cc_start: 0.8720 (t80) cc_final: 0.8398 (t80) REVERT: H 93 GLU cc_start: 0.9062 (mp0) cc_final: 0.8853 (mp0) REVERT: O 12 LYS cc_start: 0.9274 (ttmt) cc_final: 0.9049 (mtpt) REVERT: O 40 GLU cc_start: 0.9702 (tp30) cc_final: 0.9451 (tp30) REVERT: M 91 LYS cc_start: 0.6961 (pttp) cc_final: 0.6704 (pptt) REVERT: N 44 MET cc_start: 0.8929 (mmt) cc_final: 0.8498 (mmt) outliers start: 26 outliers final: 16 residues processed: 242 average time/residue: 0.8043 time to fit residues: 207.8906 Evaluate side-chains 239 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 221 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain M residue 124 PHE Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 38 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 87 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 0.2980 chunk 114 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN F 27 GLN G 24 GLN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.083039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.051090 restraints weight = 42363.032| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.69 r_work: 0.2648 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15256 Z= 0.184 Angle : 0.677 15.371 21832 Z= 0.375 Chirality : 0.042 0.387 2461 Planarity : 0.004 0.047 1752 Dihedral : 30.659 103.289 4362 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.82 % Allowed : 25.17 % Favored : 72.01 % 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: 2.42 (0.26), residues: 1021 helix: 2.52 (0.19), residues: 725 sheet: -3.35 (1.60), residues: 10 loop : -0.67 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 132 TYR 0.011 0.001 TYR D 40 PHE 0.019 0.001 PHE N 22 TRP 0.012 0.002 TRP N 33 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.18 (15256) covalent geometry : angle 0.67671 / 0.38 (21832) hydrogen bonds : bond 0.04269 / 2.79 ( 928) hydrogen bonds : angle 3.13591 / 2.30 ( 2371) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8946 (ptp-110) REVERT: A 56 LYS cc_start: 0.9445 (ttpp) cc_final: 0.9239 (ttmm) REVERT: A 59 GLU cc_start: 0.8432 (pm20) cc_final: 0.8089 (pm20) REVERT: D 35 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8257 (mm-30) REVERT: D 42 TYR cc_start: 0.8791 (t80) cc_final: 0.8448 (t80) REVERT: D 105 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8823 (mm-30) REVERT: E 59 GLU cc_start: 0.8923 (pm20) cc_final: 0.8562 (pm20) REVERT: E 129 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8162 (tmm160) REVERT: F 93 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8874 (mm110) REVERT: G 15 LYS cc_start: 0.9254 (ttmm) cc_final: 0.8936 (ttpp) REVERT: G 92 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8344 (mt-10) REVERT: G 99 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8777 (mtpp) REVERT: H 33 ARG cc_start: 0.8252 (ttm110) cc_final: 0.7586 (mtp-110) REVERT: H 35 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7976 (mt-10) REVERT: H 42 TYR cc_start: 0.8731 (t80) cc_final: 0.8403 (t80) REVERT: H 93 GLU cc_start: 0.9080 (mp0) cc_final: 0.8719 (mp0) REVERT: O 12 LYS cc_start: 0.9284 (ttmt) cc_final: 0.9032 (mtpt) REVERT: O 35 ARG cc_start: 0.9407 (mtp180) cc_final: 0.9082 (tpp80) REVERT: O 40 GLU cc_start: 0.9698 (tp30) cc_final: 0.9464 (tp30) REVERT: N 44 MET cc_start: 0.8901 (mmt) cc_final: 0.8486 (mmt) outliers start: 25 outliers final: 16 residues processed: 243 average time/residue: 0.8610 time to fit residues: 223.1539 Evaluate side-chains 242 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 223 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain M residue 124 PHE Chi-restraints excluded: chain N residue 16 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 112 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 118 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 124 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** N 38 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 = 0.3594 r_free = 0.3594 target = 0.083573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.051627 restraints weight = 42052.781| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.65 r_work: 0.2662 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15256 Z= 0.155 Angle : 0.695 14.487 21832 Z= 0.380 Chirality : 0.042 0.388 2461 Planarity : 0.005 0.048 1752 Dihedral : 30.633 102.810 4362 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.71 % Allowed : 25.96 % Favored : 71.33 % 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: 2.52 (0.26), residues: 1021 helix: 2.59 (0.19), residues: 723 sheet: -3.36 (1.59), residues: 10 loop : -0.62 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG M 132 TYR 0.011 0.001 TYR D 40 PHE 0.009 0.001 PHE E 67 TRP 0.011 0.002 TRP N 33 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (15256) covalent geometry : angle 0.69513 / 0.38 (21832) hydrogen bonds : bond 0.04083 / 2.67 ( 928) hydrogen bonds : angle 3.11628 / 2.29 ( 2371) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 237 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8904 (ptp-110) REVERT: A 56 LYS cc_start: 0.9441 (ttpp) cc_final: 0.9228 (ttmm) REVERT: A 59 GLU cc_start: 0.8403 (pm20) cc_final: 0.8049 (pm20) REVERT: D 34 LYS cc_start: 0.9107 (mmmm) cc_final: 0.8710 (mmtm) REVERT: D 35 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8197 (mm-30) REVERT: D 42 TYR cc_start: 0.8696 (t80) cc_final: 0.8322 (t80) REVERT: E 59 GLU cc_start: 0.8908 (pm20) cc_final: 0.8513 (pm20) REVERT: E 129 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8159 (tmm160) REVERT: F 93 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8784 (mm110) REVERT: G 15 LYS cc_start: 0.9202 (ttmm) cc_final: 0.8877 (ttpp) REVERT: G 92 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8280 (mt-10) REVERT: G 99 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8716 (mtpp) REVERT: H 33 ARG cc_start: 0.8256 (ttm110) cc_final: 0.7401 (mtp-110) REVERT: H 34 LYS cc_start: 0.8860 (mptt) cc_final: 0.8515 (mmtm) REVERT: H 35 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7957 (mm-30) REVERT: H 42 TYR cc_start: 0.8646 (t80) cc_final: 0.8301 (t80) REVERT: H 93 GLU cc_start: 0.9074 (mp0) cc_final: 0.8634 (mp0) REVERT: O 12 LYS cc_start: 0.9224 (ttmt) cc_final: 0.8958 (mtpt) REVERT: O 40 GLU cc_start: 0.9686 (tp30) cc_final: 0.9449 (tp30) REVERT: M 91 LYS cc_start: 0.6909 (pttp) cc_final: 0.6633 (pptt) REVERT: M 120 LYS cc_start: 0.9435 (ptpt) cc_final: 0.9103 (pttm) REVERT: N 44 MET cc_start: 0.8921 (mmt) cc_final: 0.8516 (mmt) outliers start: 24 outliers final: 13 residues processed: 249 average time/residue: 0.8046 time to fit residues: 214.5152 Evaluate side-chains 246 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 230 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain M residue 124 PHE Chi-restraints excluded: chain N residue 16 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 63 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 121 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 0.0980 chunk 91 optimal weight: 20.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN F 27 GLN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.083528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.051588 restraints weight = 42170.112| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.68 r_work: 0.2677 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15256 Z= 0.160 Angle : 0.712 15.137 21832 Z= 0.384 Chirality : 0.042 0.387 2461 Planarity : 0.005 0.068 1752 Dihedral : 30.626 102.265 4362 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.03 % Allowed : 27.20 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 2.47 (0.26), residues: 1021 helix: 2.55 (0.19), residues: 723 sheet: -3.33 (1.59), residues: 10 loop : -0.62 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG M 132 TYR 0.012 0.001 TYR E 99 PHE 0.011 0.001 PHE M 124 TRP 0.017 0.002 TRP N 33 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (15256) covalent geometry : angle 0.71202 / 0.38 (21832) hydrogen bonds : bond 0.04119 / 2.70 ( 928) hydrogen bonds : angle 3.15472 / 2.30 ( 2371) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 238 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8890 (ptp-110) REVERT: A 56 LYS cc_start: 0.9440 (ttpp) cc_final: 0.9226 (ttmm) REVERT: A 59 GLU cc_start: 0.8400 (pm20) cc_final: 0.8038 (pm20) REVERT: D 34 LYS cc_start: 0.9128 (mmmm) cc_final: 0.8689 (mmtm) REVERT: D 35 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8180 (mm-30) REVERT: D 42 TYR cc_start: 0.8693 (t80) cc_final: 0.8346 (t80) REVERT: D 86 ARG cc_start: 0.9078 (mmt90) cc_final: 0.8848 (mmt90) REVERT: D 105 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8671 (mm-30) REVERT: D 108 LYS cc_start: 0.9084 (ptpp) cc_final: 0.8643 (ptmm) REVERT: E 59 GLU cc_start: 0.8898 (pm20) cc_final: 0.8524 (pm20) REVERT: E 129 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8164 (tmm160) REVERT: F 93 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8782 (mm110) REVERT: G 15 LYS cc_start: 0.9197 (ttmm) cc_final: 0.8867 (ttpp) REVERT: G 92 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8266 (mt-10) REVERT: G 99 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8715 (mtpp) REVERT: H 33 ARG cc_start: 0.8227 (ttm110) cc_final: 0.7406 (mtp-110) REVERT: H 34 LYS cc_start: 0.8817 (mptt) cc_final: 0.8456 (mmtm) REVERT: H 35 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7956 (mm-30) REVERT: H 93 GLU cc_start: 0.9077 (mp0) cc_final: 0.8450 (mp0) REVERT: O 12 LYS cc_start: 0.9216 (ttmt) cc_final: 0.8966 (mtpt) REVERT: O 40 GLU cc_start: 0.9679 (tp30) cc_final: 0.9409 (tp30) REVERT: M 18 ARG cc_start: 0.7075 (mtm-85) cc_final: 0.6666 (mtt90) REVERT: M 91 LYS cc_start: 0.6969 (pttp) cc_final: 0.6700 (pptt) REVERT: M 120 LYS cc_start: 0.9512 (ptpt) cc_final: 0.9151 (pttm) REVERT: N 44 MET cc_start: 0.8896 (mmt) cc_final: 0.8502 (mmt) outliers start: 18 outliers final: 12 residues processed: 248 average time/residue: 0.8498 time to fit residues: 225.2680 Evaluate side-chains 249 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 234 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain M residue 124 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 73 optimal weight: 0.2980 chunk 59 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** N 38 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 = 0.3590 r_free = 0.3590 target = 0.083432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.051431 restraints weight = 42069.995| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.67 r_work: 0.2672 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15256 Z= 0.171 Angle : 0.733 16.371 21832 Z= 0.396 Chirality : 0.043 0.387 2461 Planarity : 0.005 0.069 1752 Dihedral : 30.650 103.420 4362 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.03 % Allowed : 27.54 % Favored : 70.43 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 2.42 (0.26), residues: 1021 helix: 2.51 (0.19), residues: 724 sheet: -3.32 (1.59), residues: 10 loop : -0.64 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG M 132 TYR 0.017 0.001 TYR F 88 PHE 0.010 0.001 PHE E 67 TRP 0.019 0.002 TRP N 33 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (15256) covalent geometry : angle 0.73269 / 0.40 (21832) hydrogen bonds : bond 0.04194 / 2.73 ( 928) hydrogen bonds : angle 3.22543 / 2.37 ( 2371) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 235 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8901 (ptp-110) REVERT: A 56 LYS cc_start: 0.9439 (ttpp) cc_final: 0.9228 (ttmm) REVERT: A 59 GLU cc_start: 0.8428 (pm20) cc_final: 0.8073 (pm20) REVERT: D 34 LYS cc_start: 0.9137 (mmmm) cc_final: 0.8827 (mptt) REVERT: D 35 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8145 (mm-30) REVERT: D 42 TYR cc_start: 0.8710 (t80) cc_final: 0.8359 (t80) REVERT: D 86 ARG cc_start: 0.9090 (mmt90) cc_final: 0.8858 (mmt90) REVERT: D 105 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8697 (mm-30) REVERT: D 108 LYS cc_start: 0.9113 (ptpp) cc_final: 0.8632 (pttm) REVERT: E 59 GLU cc_start: 0.8927 (pm20) cc_final: 0.8540 (pm20) REVERT: E 129 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8170 (tmm160) REVERT: F 24 ASP cc_start: 0.7733 (t0) cc_final: 0.7529 (OUTLIER) REVERT: F 93 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8774 (mm110) REVERT: G 15 LYS cc_start: 0.9213 (ttmm) cc_final: 0.8881 (ttpp) REVERT: G 92 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8299 (mt-10) REVERT: G 99 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8725 (mtpp) REVERT: H 33 ARG cc_start: 0.8222 (ttm110) cc_final: 0.7415 (mtp-110) REVERT: H 34 LYS cc_start: 0.8847 (mptt) cc_final: 0.8494 (mmtm) REVERT: H 35 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7980 (mm-30) REVERT: H 93 GLU cc_start: 0.9080 (mp0) cc_final: 0.8432 (mp0) REVERT: O 12 LYS cc_start: 0.9224 (ttmt) cc_final: 0.9011 (mtpt) REVERT: O 40 GLU cc_start: 0.9666 (tp30) cc_final: 0.9387 (tp30) REVERT: M 18 ARG cc_start: 0.7129 (mtm-85) cc_final: 0.6730 (mtt90) REVERT: M 91 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6703 (pptt) REVERT: M 115 LYS cc_start: 0.9697 (tppt) cc_final: 0.9460 (ttpm) REVERT: N 44 MET cc_start: 0.8901 (mmt) cc_final: 0.8487 (mmt) outliers start: 18 outliers final: 13 residues processed: 244 average time/residue: 0.8377 time to fit residues: 218.3871 Evaluate side-chains 247 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 231 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain M residue 91 LYS Chi-restraints excluded: chain M residue 124 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 46 optimal weight: 0.6980 chunk 62 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.084022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.052187 restraints weight = 42584.476| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.74 r_work: 0.2695 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15256 Z= 0.153 Angle : 0.741 17.252 21832 Z= 0.398 Chirality : 0.042 0.378 2461 Planarity : 0.005 0.051 1752 Dihedral : 30.608 105.825 4362 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.92 % Allowed : 27.99 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 2.37 (0.26), residues: 1021 helix: 2.47 (0.19), residues: 723 sheet: -3.30 (1.58), residues: 10 loop : -0.64 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG O 30 TYR 0.013 0.001 TYR D 37 PHE 0.009 0.001 PHE E 67 TRP 0.022 0.002 TRP N 33 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (15256) covalent geometry : angle 0.74098 / 0.40 (21832) hydrogen bonds : bond 0.04108 / 2.69 ( 928) hydrogen bonds : angle 3.27570 / 2.40 ( 2371) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6223.70 seconds wall clock time: 106 minutes 33.88 seconds (6393.88 seconds total)