Starting phenix.real_space_refine on Thu Aug 6 09:00:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9si3_54924/08_2026/9si3_54924.cif Found real_map, /net/cci-nas-00/data/ceres_data/9si3_54924/08_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_54924/08_2026/9si3_54924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9si3_54924/08_2026/9si3_54924.map" model { file = "/net/cci-nas-00/data/ceres_data/9si3_54924/08_2026/9si3_54924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9si3_54924/08_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-2.2rc3-6140/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: 3.07, per 1000 atoms: 0.21 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: 1.20 Conformation dependent library (CDL) restraints added in 400.6 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: 2.01 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: 2.98 Time building geometry restraints manager: 1.63 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: 21380 2.31 - 4.63: 420 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.030 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.620 ------------------------------------------------------------------------------- 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= 0.494 Angle : 0.749 11.572 21832 Z= 0.645 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 0.74874 / 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 : 0.368 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: 0.8206 (t80) outliers start: 0 outliers final: 1 residues processed: 310 average time/residue: 0.8156 time to fit residues: 270.6968 Evaluate side-chains 242 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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: 9.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 9.9990 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: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 113 HIS C 24 GLN F 75 HIS N 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.082951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.051185 restraints weight = 42105.058| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.72 r_work: 0.2639 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15256 Z= 0.209 Angle : 0.699 12.576 21832 Z= 0.391 Chirality : 0.044 0.337 2461 Planarity : 0.005 0.047 1752 Dihedral : 30.270 105.446 4364 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.06 % Allowed : 23.02 % Favored : 72.91 % 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: 2.41 (0.26), residues: 1021 helix: 2.51 (0.19), residues: 722 sheet: -2.75 (1.69), residues: 10 loop : -0.64 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 29 TYR 0.011 0.001 TYR D 40 PHE 0.011 0.001 PHE A 67 TRP 0.014 0.002 TRP M 25 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.21 (15256) covalent geometry : angle 0.69931 / 0.39 (21832) hydrogen bonds : bond 0.04871 / 3.14 ( 928) hydrogen bonds : angle 3.25091 / 2.38 ( 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 274 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 238 time to evaluate : 0.414 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: A 42 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8652 (ptp90) REVERT: A 56 LYS cc_start: 0.9411 (ttpp) cc_final: 0.9165 (ttmm) REVERT: A 59 GLU cc_start: 0.8284 (pm20) cc_final: 0.7923 (pm20) REVERT: A 73 GLU cc_start: 0.8944 (tt0) cc_final: 0.8378 (tt0) REVERT: B 25 ASN cc_start: 0.8972 (m110) cc_final: 0.8351 (m110) REVERT: D 34 LYS cc_start: 0.9166 (mmmm) cc_final: 0.8870 (mppt) REVERT: D 35 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8197 (mm-30) REVERT: D 68 ASP cc_start: 0.9144 (t0) cc_final: 0.8918 (t0) REVERT: D 105 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8548 (mt-10) REVERT: F 77 LYS cc_start: 0.9523 (OUTLIER) cc_final: 0.9245 (mtpt) REVERT: G 20 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8884 (mtt-85) REVERT: G 92 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8360 (mt-10) REVERT: H 33 ARG cc_start: 0.8149 (ttm110) cc_final: 0.7409 (mtp-110) REVERT: H 42 TYR cc_start: 0.8580 (t80) cc_final: 0.8236 (t80) REVERT: H 93 GLU cc_start: 0.9110 (mp0) cc_final: 0.8899 (mp0) REVERT: O 12 LYS cc_start: 0.9183 (ttmt) cc_final: 0.8909 (mtpt) REVERT: N 44 MET cc_start: 0.8912 (mmt) cc_final: 0.8706 (mmt) outliers start: 36 outliers final: 9 residues processed: 255 average time/residue: 0.7241 time to fit residues: 197.8458 Evaluate side-chains 246 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 234 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 89 optimal weight: 30.0000 chunk 41 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN F 27 GLN ** M 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.083527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.051223 restraints weight = 42379.622| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.73 r_work: 0.2651 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15256 Z= 0.166 Angle : 0.657 12.866 21832 Z= 0.370 Chirality : 0.043 0.340 2461 Planarity : 0.004 0.044 1752 Dihedral : 30.393 104.260 4362 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.05 % Allowed : 23.48 % Favored : 73.48 % 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: 2.53 (0.19), residues: 725 sheet: -2.96 (1.65), residues: 10 loop : -0.68 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 132 TYR 0.011 0.001 TYR D 40 PHE 0.015 0.001 PHE M 22 TRP 0.011 0.002 TRP M 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.17 (15256) covalent geometry : angle 0.65682 / 0.37 (21832) hydrogen bonds : bond 0.04374 / 2.84 ( 928) hydrogen bonds : angle 3.11909 / 2.29 ( 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 265 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 238 time to evaluate : 0.409 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: 0.9071 (OUTLIER) cc_final: 0.8653 (ptp90) REVERT: A 56 LYS cc_start: 0.9396 (ttpp) cc_final: 0.9160 (ttmm) REVERT: A 59 GLU cc_start: 0.8302 (pm20) cc_final: 0.7927 (pm20) REVERT: D 34 LYS cc_start: 0.9170 (mmmm) cc_final: 0.8728 (mmtm) REVERT: D 35 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8185 (mm-30) REVERT: D 68 ASP cc_start: 0.9202 (t0) cc_final: 0.8950 (t0) REVERT: D 105 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8491 (mt-10) REVERT: E 59 GLU cc_start: 0.8608 (pm20) cc_final: 0.8177 (pm20) REVERT: E 129 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8109 (tmm160) REVERT: F 77 LYS cc_start: 0.9525 (OUTLIER) cc_final: 0.9262 (mtpt) REVERT: F 92 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8950 (mtp85) REVERT: G 92 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8219 (mt-10) REVERT: H 35 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8057 (mt-10) REVERT: H 42 TYR cc_start: 0.8509 (t80) cc_final: 0.8179 (t80) REVERT: H 93 GLU cc_start: 0.9161 (mp0) cc_final: 0.8885 (mp0) REVERT: H 105 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8598 (mt-10) REVERT: O 10 VAL cc_start: 0.9488 (t) cc_final: 0.9286 (p) REVERT: O 12 LYS cc_start: 0.9197 (ttmt) cc_final: 0.8865 (mtpt) REVERT: O 17 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8315 (ttt180) REVERT: O 20 LYS cc_start: 0.9199 (pptt) cc_final: 0.8980 (pptt) REVERT: N 44 MET cc_start: 0.8980 (mmt) cc_final: 0.8501 (mmt) outliers start: 27 outliers final: 11 residues processed: 250 average time/residue: 0.7548 time to fit residues: 201.9190 Evaluate side-chains 244 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 228 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 E residue 129 ARG 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 F residue 92 ARG 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 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: 5.9990 chunk 101 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 chunk 126 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 112 GLN M 11 GLN ** M 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.082104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.049980 restraints weight = 42566.661| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.70 r_work: 0.2614 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15256 Z= 0.232 Angle : 0.693 10.722 21832 Z= 0.381 Chirality : 0.044 0.357 2461 Planarity : 0.005 0.074 1752 Dihedral : 30.592 103.822 4362 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.84 % Allowed : 22.46 % Favored : 73.70 % 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: 2.51 (0.19), residues: 725 sheet: -3.19 (1.62), residues: 10 loop : -0.75 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 92 TYR 0.011 0.001 TYR D 40 PHE 0.015 0.002 PHE M 124 TRP 0.009 0.001 TRP M 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.23 (15256) covalent geometry : angle 0.69318 / 0.38 (21832) hydrogen bonds : bond 0.04851 / 3.15 ( 928) hydrogen bonds : angle 3.16706 / 2.33 ( 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 264 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 230 time to evaluate : 0.398 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: A 42 ARG cc_start: 0.9209 (OUTLIER) cc_final: 0.8760 (ptp90) REVERT: A 56 LYS cc_start: 0.9440 (ttpp) cc_final: 0.9228 (ttmm) REVERT: A 59 GLU cc_start: 0.8453 (pm20) cc_final: 0.8136 (pm20) REVERT: A 106 ASP cc_start: 0.9344 (m-30) cc_final: 0.8915 (m-30) REVERT: D 35 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8216 (mm-30) REVERT: D 68 ASP cc_start: 0.9223 (t0) cc_final: 0.8976 (t0) REVERT: E 59 GLU cc_start: 0.8722 (pm20) cc_final: 0.8349 (pm20) REVERT: E 129 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8150 (tmm160) REVERT: F 77 LYS cc_start: 0.9496 (OUTLIER) cc_final: 0.9273 (mtpt) REVERT: F 92 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.9013 (mtp85) REVERT: G 92 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8309 (mt-10) REVERT: H 33 ARG cc_start: 0.8239 (ttm110) cc_final: 0.7588 (mtp-110) REVERT: H 35 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7971 (mt-10) REVERT: O 12 LYS cc_start: 0.9326 (ttmt) cc_final: 0.8982 (mtpt) REVERT: O 20 LYS cc_start: 0.9268 (pptt) cc_final: 0.9028 (pptt) REVERT: M 91 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6545 (pptt) REVERT: N 44 MET cc_start: 0.9007 (mmt) cc_final: 0.8501 (mmt) outliers start: 34 outliers final: 12 residues processed: 248 average time/residue: 0.7552 time to fit residues: 200.2389 Evaluate side-chains 238 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 59 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain O residue 25 LEU 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: 0.9980 chunk 24 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN F 27 GLN G 24 GLN H 47 GLN O 44 GLN N 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.083137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.051085 restraints weight = 42426.117| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.70 r_work: 0.2653 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15256 Z= 0.149 Angle : 0.659 11.326 21832 Z= 0.367 Chirality : 0.042 0.374 2461 Planarity : 0.004 0.042 1752 Dihedral : 30.572 102.999 4362 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.50 % Allowed : 23.59 % Favored : 72.91 % 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: 2.45 (0.26), residues: 1021 helix: 2.55 (0.19), residues: 725 sheet: -3.34 (1.60), residues: 10 loop : -0.71 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 30 TYR 0.012 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 0.00268 / 0.15 (15256) covalent geometry : angle 0.65948 / 0.37 (21832) hydrogen bonds : bond 0.04106 / 2.67 ( 928) hydrogen bonds : angle 3.05702 / 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 273 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8786 (ptp90) REVERT: A 56 LYS cc_start: 0.9428 (ttpp) cc_final: 0.9218 (ttmm) REVERT: A 59 GLU cc_start: 0.8462 (pm20) cc_final: 0.8140 (pm20) REVERT: D 34 LYS cc_start: 0.9228 (mmmm) cc_final: 0.8955 (mmtm) REVERT: D 35 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8266 (mm-30) REVERT: D 56 SER cc_start: 0.9525 (OUTLIER) cc_final: 0.9210 (p) REVERT: D 85 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9222 (mppt) REVERT: D 105 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8462 (mt-10) REVERT: E 59 GLU cc_start: 0.8779 (pm20) cc_final: 0.8402 (pm20) REVERT: E 129 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8133 (tmm160) REVERT: F 92 ARG cc_start: 0.9283 (OUTLIER) cc_final: 0.8936 (mtp85) REVERT: G 92 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8272 (mt-10) REVERT: G 99 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8762 (mtpp) REVERT: H 33 ARG cc_start: 0.8207 (ttm110) cc_final: 0.7527 (mtp-110) REVERT: H 35 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7955 (mt-10) REVERT: H 93 GLU cc_start: 0.9096 (mp0) cc_final: 0.8811 (mp0) REVERT: O 12 LYS cc_start: 0.9310 (ttmt) cc_final: 0.9016 (mtpt) REVERT: O 20 LYS cc_start: 0.9262 (pptt) cc_final: 0.9003 (pptt) REVERT: O 35 ARG cc_start: 0.9326 (OUTLIER) cc_final: 0.8901 (tpp80) REVERT: O 40 GLU cc_start: 0.9579 (tp30) cc_final: 0.9347 (tp30) REVERT: M 91 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6578 (pptt) REVERT: M 120 LYS cc_start: 0.9530 (ptpt) cc_final: 0.9150 (pttm) REVERT: M 121 LYS cc_start: 0.9123 (pptt) cc_final: 0.8918 (pptt) REVERT: N 38 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8572 (tp-100) REVERT: N 44 MET cc_start: 0.9015 (mmt) cc_final: 0.8499 (mmt) outliers start: 31 outliers final: 9 residues processed: 255 average time/residue: 0.8415 time to fit residues: 229.5927 Evaluate side-chains 246 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 228 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 D residue 56 SER Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 35 ARG Chi-restraints excluded: chain M residue 91 LYS Chi-restraints excluded: chain M residue 124 PHE Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 38 GLN 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: 0.9990 chunk 67 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN G 24 GLN G 104 GLN ** M 118 ASN ** 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 = 0.3557 r_free = 0.3557 target = 0.081849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.049629 restraints weight = 42597.519| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.70 r_work: 0.2610 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15256 Z= 0.246 Angle : 0.706 12.475 21832 Z= 0.385 Chirality : 0.044 0.380 2461 Planarity : 0.005 0.071 1752 Dihedral : 30.684 102.684 4362 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.18 % Allowed : 23.70 % Favored : 72.12 % 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: 2.39 (0.26), residues: 1021 helix: 2.52 (0.19), residues: 725 sheet: -3.41 (1.61), residues: 10 loop : -0.76 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 132 TYR 0.011 0.002 TYR E 99 PHE 0.012 0.001 PHE A 67 TRP 0.006 0.001 TRP M 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.25 (15256) covalent geometry : angle 0.70607 / 0.38 (21832) hydrogen bonds : bond 0.04830 / 3.14 ( 928) hydrogen bonds : angle 3.15685 / 2.31 ( 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 263 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 0.457 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 56 LYS cc_start: 0.9444 (ttpp) cc_final: 0.9242 (ttmm) REVERT: A 59 GLU cc_start: 0.8521 (pm20) cc_final: 0.8186 (pm20) REVERT: A 106 ASP cc_start: 0.9347 (m-30) cc_final: 0.8949 (m-30) REVERT: D 34 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8943 (mmtm) REVERT: D 35 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8165 (mm-30) REVERT: D 68 ASP cc_start: 0.9193 (t0) cc_final: 0.8983 (t0) REVERT: D 105 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8402 (mt-10) REVERT: E 59 GLU cc_start: 0.8840 (pm20) cc_final: 0.8453 (pm20) REVERT: E 129 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8168 (tmm160) REVERT: F 92 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.9014 (mtp85) REVERT: G 15 LYS cc_start: 0.9204 (ttmm) cc_final: 0.8861 (ttpp) REVERT: G 92 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8351 (mt-10) REVERT: G 99 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8810 (mtpp) REVERT: H 93 GLU cc_start: 0.9119 (mp0) cc_final: 0.8837 (mp0) REVERT: O 12 LYS cc_start: 0.9330 (ttmt) cc_final: 0.9002 (mtpt) REVERT: O 20 LYS cc_start: 0.9235 (pptt) cc_final: 0.9019 (pptt) REVERT: M 120 LYS cc_start: 0.9514 (ptpt) cc_final: 0.9202 (pttp) REVERT: N 44 MET cc_start: 0.9036 (mmt) cc_final: 0.8542 (mmt) outliers start: 37 outliers final: 19 residues processed: 241 average time/residue: 0.7390 time to fit residues: 190.5848 Evaluate side-chains 244 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 222 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 59 THR 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 F residue 92 ARG Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 104 GLN 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 112 LYS 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 42 GLU 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: 9.9990 chunk 124 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 50 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 104 GLN ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3586 r_free = 0.3586 target = 0.083106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.051117 restraints weight = 42295.275| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.71 r_work: 0.2655 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.2221 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= 0.144 Angle : 0.665 12.229 21832 Z= 0.370 Chirality : 0.042 0.378 2461 Planarity : 0.005 0.046 1752 Dihedral : 30.629 101.794 4362 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.82 % Allowed : 25.51 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.48 (0.26), residues: 1021 helix: 2.57 (0.19), residues: 725 sheet: -3.53 (1.59), residues: 10 loop : -0.67 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG M 132 TYR 0.012 0.001 TYR D 40 PHE 0.016 0.001 PHE M 58 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 0.00256 / 0.14 (15256) covalent geometry : angle 0.66539 / 0.37 (21832) hydrogen bonds : bond 0.04018 / 2.62 ( 928) hydrogen bonds : angle 3.06948 / 2.25 ( 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 266 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 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: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9428 (ttpp) cc_final: 0.9228 (ttmm) REVERT: A 59 GLU cc_start: 0.8504 (pm20) cc_final: 0.8156 (pm20) REVERT: D 34 LYS cc_start: 0.9219 (mmmm) cc_final: 0.8934 (mmtm) REVERT: D 35 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8164 (mm-30) REVERT: D 105 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8509 (mt-10) REVERT: E 59 GLU cc_start: 0.8831 (pm20) cc_final: 0.8418 (pm20) REVERT: E 129 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8139 (tmm160) REVERT: F 92 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8955 (mtp85) REVERT: F 93 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8863 (mm110) REVERT: G 15 LYS cc_start: 0.9220 (ttmm) cc_final: 0.8873 (ttpp) REVERT: G 92 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8352 (mt-10) REVERT: G 99 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8757 (mtpp) REVERT: H 33 ARG cc_start: 0.8275 (ttm110) cc_final: 0.7587 (mtp-110) REVERT: H 35 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8063 (mm-30) REVERT: O 12 LYS cc_start: 0.9282 (ttmt) cc_final: 0.9043 (mtpt) REVERT: O 20 LYS cc_start: 0.9240 (pptt) cc_final: 0.8927 (pptt) REVERT: O 35 ARG cc_start: 0.9415 (mtp180) cc_final: 0.9002 (tpp80) REVERT: M 91 LYS cc_start: 0.6855 (pttp) cc_final: 0.6562 (pptt) REVERT: M 120 LYS cc_start: 0.9557 (ptpt) cc_final: 0.9163 (pttp) REVERT: N 44 MET cc_start: 0.9096 (mmt) cc_final: 0.8531 (mmt) outliers start: 25 outliers final: 12 residues processed: 252 average time/residue: 0.8001 time to fit residues: 215.7406 Evaluate side-chains 242 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 227 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 92 ARG 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 124 PHE Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 42 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 112 optimal weight: 0.0040 chunk 69 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 56 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 94 ASN F 27 GLN M 56 GLN ** M 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3592 r_free = 0.3592 target = 0.083439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.051480 restraints weight = 42116.847| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.71 r_work: 0.2677 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.2320 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= 0.144 Angle : 0.678 12.542 21832 Z= 0.375 Chirality : 0.042 0.383 2461 Planarity : 0.004 0.043 1752 Dihedral : 30.553 100.826 4362 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.16 % Allowed : 26.52 % Favored : 70.32 % 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: 2.46 (0.26), residues: 1021 helix: 2.55 (0.19), residues: 725 sheet: -3.63 (1.59), residues: 10 loop : -0.65 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG M 132 TYR 0.012 0.001 TYR D 40 PHE 0.013 0.001 PHE M 61 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 0.00261 / 0.14 (15256) covalent geometry : angle 0.67821 / 0.38 (21832) hydrogen bonds : bond 0.04023 / 2.63 ( 928) hydrogen bonds : angle 3.12103 / 2.27 ( 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 267 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 0.437 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 56 LYS cc_start: 0.9432 (ttpp) cc_final: 0.9225 (ttmm) REVERT: A 59 GLU cc_start: 0.8449 (pm20) cc_final: 0.8099 (pm20) REVERT: C 116 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9132 (mm) REVERT: D 34 LYS cc_start: 0.9213 (mmmm) cc_final: 0.8910 (mmtm) REVERT: D 35 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8152 (mm-30) REVERT: D 105 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8454 (mt-10) REVERT: E 59 GLU cc_start: 0.8814 (pm20) cc_final: 0.8438 (pm20) REVERT: E 129 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8138 (tmm160) REVERT: F 24 ASP cc_start: 0.7934 (t0) cc_final: 0.7713 (OUTLIER) REVERT: F 92 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8959 (mtp85) REVERT: F 93 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8782 (mm110) REVERT: G 15 LYS cc_start: 0.9176 (ttmm) cc_final: 0.8824 (ttpp) REVERT: G 92 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8313 (mt-10) REVERT: H 33 ARG cc_start: 0.8237 (ttm110) cc_final: 0.7560 (mtp-110) REVERT: H 35 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8055 (mm-30) REVERT: H 93 GLU cc_start: 0.9073 (mp0) cc_final: 0.8479 (mp0) REVERT: O 20 LYS cc_start: 0.9219 (pptt) cc_final: 0.8907 (pptt) REVERT: O 35 ARG cc_start: 0.9404 (mtp180) cc_final: 0.8817 (tpp80) REVERT: M 91 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6704 (pptt) REVERT: M 120 LYS cc_start: 0.9559 (ptpt) cc_final: 0.9302 (pttp) REVERT: N 44 MET cc_start: 0.9116 (mmt) cc_final: 0.8545 (mmt) outliers start: 28 outliers final: 14 residues processed: 251 average time/residue: 0.8128 time to fit residues: 218.2699 Evaluate side-chains 248 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 231 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 82 THR Chi-restraints excluded: chain F residue 92 ARG 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 58 PHE Chi-restraints excluded: chain M residue 91 LYS Chi-restraints excluded: chain M residue 124 PHE Chi-restraints excluded: chain N residue 42 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 24 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 = 0.3573 r_free = 0.3573 target = 0.082402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.050264 restraints weight = 42365.716| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.70 r_work: 0.2634 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 15256 Z= 0.212 Angle : 0.725 17.553 21832 Z= 0.390 Chirality : 0.043 0.381 2461 Planarity : 0.004 0.047 1752 Dihedral : 30.644 100.479 4362 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.37 % Allowed : 27.77 % Favored : 69.86 % 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: 2.46 (0.26), residues: 1021 helix: 2.55 (0.19), residues: 725 sheet: -3.63 (1.60), residues: 10 loop : -0.67 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG M 132 TYR 0.014 0.001 TYR F 88 PHE 0.010 0.001 PHE A 67 TRP 0.021 0.003 TRP N 33 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.21 (15256) covalent geometry : angle 0.72482 / 0.39 (21832) hydrogen bonds : bond 0.04478 / 2.93 ( 928) hydrogen bonds : angle 3.20400 / 2.33 ( 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 253 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 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 59 GLU cc_start: 0.8511 (pm20) cc_final: 0.8172 (pm20) REVERT: A 106 ASP cc_start: 0.9321 (m-30) cc_final: 0.8919 (m-30) REVERT: C 116 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9170 (mm) REVERT: D 35 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8142 (mm-30) REVERT: D 105 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8521 (mt-10) REVERT: E 59 GLU cc_start: 0.8867 (pm20) cc_final: 0.8469 (pm20) REVERT: E 129 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8211 (tmm160) REVERT: F 92 ARG cc_start: 0.9321 (OUTLIER) cc_final: 0.8989 (mtp85) REVERT: F 93 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8801 (mm110) REVERT: G 15 LYS cc_start: 0.9238 (ttmm) cc_final: 0.8897 (ttpp) REVERT: G 92 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8379 (mt-10) REVERT: G 99 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8751 (mtpp) REVERT: H 33 ARG cc_start: 0.8242 (ttm110) cc_final: 0.7446 (mtp-110) REVERT: H 34 LYS cc_start: 0.8848 (mptt) cc_final: 0.8510 (mmtm) REVERT: H 35 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8041 (mm-30) REVERT: H 93 GLU cc_start: 0.9081 (mp0) cc_final: 0.8487 (mp0) REVERT: O 35 ARG cc_start: 0.9360 (mtp180) cc_final: 0.8987 (tpp80) REVERT: M 91 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6641 (pptt) REVERT: M 120 LYS cc_start: 0.9608 (ptpt) cc_final: 0.9356 (pttp) REVERT: N 44 MET cc_start: 0.9127 (mmt) cc_final: 0.8616 (mmt) outliers start: 21 outliers final: 15 residues processed: 241 average time/residue: 0.8641 time to fit residues: 222.0088 Evaluate side-chains 248 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 92 ARG 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 10 VAL 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 Chi-restraints excluded: chain N residue 42 GLU 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: 0.7980 chunk 95 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN F 27 GLN G 24 GLN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.082829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.050717 restraints weight = 42244.511| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.68 r_work: 0.2644 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15256 Z= 0.177 Angle : 0.744 16.448 21832 Z= 0.399 Chirality : 0.044 0.386 2461 Planarity : 0.005 0.069 1752 Dihedral : 30.666 101.686 4362 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.37 % Allowed : 28.22 % Favored : 69.41 % 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: 2.40 (0.26), residues: 1021 helix: 2.51 (0.19), residues: 724 sheet: -3.74 (1.61), residues: 10 loop : -0.65 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG M 132 TYR 0.016 0.001 TYR F 88 PHE 0.018 0.001 PHE N 45 TRP 0.016 0.002 TRP N 33 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.18 (15256) covalent geometry : angle 0.74409 / 0.40 (21832) hydrogen bonds : bond 0.04217 / 2.75 ( 928) hydrogen bonds : angle 3.20242 / 2.36 ( 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 251 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8537 (pm20) cc_final: 0.8202 (pm20) REVERT: A 106 ASP cc_start: 0.9314 (m-30) cc_final: 0.8917 (m-30) REVERT: C 116 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9144 (mm) REVERT: D 35 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8167 (mm-30) REVERT: D 105 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8488 (mt-10) REVERT: E 59 GLU cc_start: 0.8850 (pm20) cc_final: 0.8488 (pm20) REVERT: E 129 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8201 (tmm160) REVERT: F 24 ASP cc_start: 0.7881 (t0) cc_final: 0.7634 (t0) REVERT: F 92 ARG cc_start: 0.9301 (OUTLIER) cc_final: 0.8971 (mtp85) REVERT: F 93 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8788 (mm110) REVERT: G 15 LYS cc_start: 0.9238 (ttmm) cc_final: 0.8898 (ttpp) REVERT: G 92 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8332 (mt-10) REVERT: G 99 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8735 (mtpp) REVERT: H 33 ARG cc_start: 0.8244 (ttm110) cc_final: 0.7448 (mtp-110) REVERT: H 34 LYS cc_start: 0.8844 (mptt) cc_final: 0.8511 (mmtm) REVERT: H 35 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8035 (mm-30) REVERT: H 93 GLU cc_start: 0.9079 (mp0) cc_final: 0.8492 (mp0) REVERT: O 35 ARG cc_start: 0.9386 (mtp180) cc_final: 0.9100 (tpp80) REVERT: M 91 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6681 (pptt) REVERT: M 116 GLU cc_start: 0.9530 (mm-30) cc_final: 0.8909 (pt0) REVERT: M 120 LYS cc_start: 0.9555 (ptpt) cc_final: 0.9294 (pttp) REVERT: N 44 MET cc_start: 0.9026 (mmt) cc_final: 0.8560 (mmt) outliers start: 21 outliers final: 13 residues processed: 239 average time/residue: 0.8215 time to fit residues: 209.7581 Evaluate side-chains 246 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 228 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain O residue 10 VAL 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 Chi-restraints excluded: chain N residue 42 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 46 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 0.0030 chunk 16 optimal weight: 3.9990 chunk 116 optimal weight: 0.3980 chunk 107 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.083116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.051161 restraints weight = 42566.365| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.69 r_work: 0.2668 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15256 Z= 0.155 Angle : 0.719 12.643 21832 Z= 0.393 Chirality : 0.043 0.382 2461 Planarity : 0.005 0.072 1752 Dihedral : 30.620 103.658 4362 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.14 % Allowed : 28.33 % Favored : 69.53 % 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: 2.42 (0.26), residues: 1021 helix: 2.51 (0.19), residues: 724 sheet: -4.01 (1.58), residues: 10 loop : -0.63 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG M 132 TYR 0.015 0.001 TYR F 88 PHE 0.013 0.001 PHE N 45 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 0.00293 / 0.16 (15256) covalent geometry : angle 0.71854 / 0.39 (21832) hydrogen bonds : bond 0.04051 / 2.65 ( 928) hydrogen bonds : angle 3.20439 / 2.34 ( 2371) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6291.39 seconds wall clock time: 107 minutes 30.63 seconds (6450.63 seconds total)