Starting phenix.real_space_refine on Thu Feb 5 01:54:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9si3_54924/02_2026/9si3_54924.cif Found real_map, /net/cci-nas-00/data/ceres_data/9si3_54924/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9si3_54924/02_2026/9si3_54924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9si3_54924/02_2026/9si3_54924.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9si3_54924/02_2026/9si3_54924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9si3_54924/02_2026/9si3_54924.map" } 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-2.0-5952/lib/python3.9/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: 2.79, per 1000 atoms: 0.19 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: 1.13 Conformation dependent library (CDL) restraints added in 413.8 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: 2.17 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: 2.70 Time building geometry restraints manager: 1.51 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=" N ASN O 14 " pdb=" CA ASN O 14 " ideal model delta sigma weight residual 1.459 1.484 -0.024 1.18e-02 7.18e+03 4.28e+00 bond pdb=" CA THR O 13 " pdb=" C THR O 13 " ideal model delta sigma weight residual 1.524 1.499 0.025 1.32e-02 5.74e+03 3.45e+00 bond pdb=" N SER O 15 " pdb=" CA SER O 15 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.23e-02 6.61e+03 3.11e+00 bond pdb=" N LEU O 16 " pdb=" CA LEU O 16 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.20e-02 6.94e+03 2.69e+00 ... (remaining 15251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 21654 2.31 - 4.63: 146 4.63 - 6.94: 25 6.94 - 9.26: 3 9.26 - 11.57: 4 Bond angle restraints: 21832 Sorted by residual: angle pdb=" CA THR O 13 " pdb=" CB THR O 13 " pdb=" OG1 THR O 13 " ideal model delta sigma weight residual 109.60 103.48 6.12 1.50e+00 4.44e-01 1.66e+01 angle pdb=" N THR O 13 " pdb=" CA THR O 13 " pdb=" C THR O 13 " ideal model delta sigma weight residual 111.69 107.07 4.62 1.23e+00 6.61e-01 1.41e+01 angle pdb=" N LYS M 112 " pdb=" CA LYS M 112 " pdb=" CB LYS M 112 " ideal model delta sigma weight residual 110.30 116.03 -5.73 1.54e+00 4.22e-01 1.38e+01 angle pdb=" N ASN M 118 " pdb=" CA ASN M 118 " pdb=" CB ASN M 118 " ideal model delta sigma weight residual 110.30 116.02 -5.72 1.54e+00 4.22e-01 1.38e+01 angle pdb=" CB MET N 20 " pdb=" CG MET N 20 " pdb=" SD MET N 20 " ideal model delta sigma weight residual 112.70 123.69 -10.99 3.00e+00 1.11e-01 1.34e+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 - 0.027: 1601 0.027 - 0.055: 600 0.055 - 0.082: 182 0.082 - 0.110: 55 0.110 - 0.137: 23 Chirality restraints: 2461 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CB ILE N 37 " pdb=" CA ILE N 37 " pdb=" CG1 ILE N 37 " pdb=" CG2 ILE N 37 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE C 111 " pdb=" N ILE C 111 " pdb=" C ILE C 111 " pdb=" CB ILE C 111 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-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: 3.730 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: 0.300 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.500 Find NCS groups from input model: 0.140 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:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 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 : 0.004 0.048 15256 Z= 0.178 Angle : 0.598 11.572 21832 Z= 0.348 Chirality : 0.034 0.137 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 covalent geometry : bond 0.00387 (15256) covalent geometry : angle 0.59756 (21832) hydrogen bonds : bond 0.10512 ( 928) hydrogen bonds : angle 3.61792 ( 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 : 0.405 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: 0.7381 time to fit residues: 244.7046 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 : 0.371 ------------------------------------------------------------------------------- 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: 4.9990 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: 6.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 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... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN A 76 GLN A 113 HIS C 24 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 = 0.3593 r_free = 0.3593 target = 0.083959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.052201 restraints weight = 42223.222| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.73 r_work: 0.2666 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15256 Z= 0.174 Angle : 0.594 11.171 21832 Z= 0.337 Chirality : 0.034 0.354 2461 Planarity : 0.005 0.045 1752 Dihedral : 30.042 102.646 4364 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.06 % Allowed : 21.67 % Favored : 74.27 % 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: 2.65 (0.26), residues: 1021 helix: 2.69 (0.19), residues: 722 sheet: -2.78 (1.66), residues: 10 loop : -0.55 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 29 TYR 0.010 0.001 TYR D 40 PHE 0.011 0.001 PHE N 45 TRP 0.013 0.002 TRP M 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00383 (15256) covalent geometry : angle 0.59399 (21832) hydrogen bonds : bond 0.03941 ( 928) hydrogen bonds : angle 3.01626 ( 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 285 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 249 time to evaluate : 0.267 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: 0.9085 (OUTLIER) cc_final: 0.8792 (ptp-110) REVERT: A 56 LYS cc_start: 0.9398 (ttpp) cc_final: 0.9145 (ttmm) REVERT: A 59 GLU cc_start: 0.8263 (pm20) cc_final: 0.7894 (pm20) REVERT: A 73 GLU cc_start: 0.8925 (tt0) cc_final: 0.8347 (tt0) REVERT: B 25 ASN cc_start: 0.9027 (m110) cc_final: 0.8405 (m110) REVERT: D 34 LYS cc_start: 0.9196 (mmmm) cc_final: 0.8890 (mppt) REVERT: D 35 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8164 (mm-30) REVERT: D 92 ARG cc_start: 0.8735 (mtm-85) cc_final: 0.8347 (ttp80) REVERT: D 105 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8496 (mt-10) REVERT: E 99 TYR cc_start: 0.9430 (t80) cc_final: 0.9225 (t80) REVERT: F 59 LYS cc_start: 0.9272 (tttm) cc_final: 0.9044 (tppp) REVERT: F 77 LYS cc_start: 0.9526 (OUTLIER) cc_final: 0.9257 (mtpt) REVERT: F 92 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8959 (mtp85) REVERT: G 92 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8279 (mt-10) REVERT: H 33 ARG cc_start: 0.8153 (ttm110) cc_final: 0.7448 (mtp-110) REVERT: H 42 TYR cc_start: 0.8527 (t80) cc_final: 0.8196 (t80) REVERT: H 93 GLU cc_start: 0.9177 (mp0) cc_final: 0.8916 (mp0) REVERT: O 12 LYS cc_start: 0.9186 (ttmt) cc_final: 0.8913 (mtpt) REVERT: O 20 LYS cc_start: 0.9199 (ptmt) cc_final: 0.8993 (pptt) REVERT: N 44 MET cc_start: 0.8821 (mmt) cc_final: 0.8540 (mmt) outliers start: 36 outliers final: 7 residues processed: 268 average time/residue: 0.7846 time to fit residues: 224.7954 Evaluate side-chains 250 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 240 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 61 LEU 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 F residue 92 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 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: 1.9990 chunk 109 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN F 27 GLN O 44 GLN N 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.083613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.051732 restraints weight = 42303.841| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.71 r_work: 0.2662 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15256 Z= 0.178 Angle : 0.584 10.982 21832 Z= 0.332 Chirality : 0.034 0.332 2461 Planarity : 0.004 0.041 1752 Dihedral : 30.119 99.914 4362 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.82 % Allowed : 22.91 % Favored : 74.27 % 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: 2.69 (0.26), residues: 1021 helix: 2.72 (0.19), residues: 725 sheet: -2.96 (1.63), residues: 10 loop : -0.59 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 132 TYR 0.010 0.001 TYR D 40 PHE 0.009 0.001 PHE E 67 TRP 0.010 0.002 TRP M 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00394 (15256) covalent geometry : angle 0.58365 (21832) hydrogen bonds : bond 0.03783 ( 928) hydrogen bonds : angle 2.98361 ( 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 268 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 243 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.9215 (OUTLIER) cc_final: 0.8937 (ptp-110) REVERT: A 56 LYS cc_start: 0.9433 (ttpp) cc_final: 0.9203 (ttmm) REVERT: A 59 GLU cc_start: 0.8368 (pm20) cc_final: 0.8077 (pm20) REVERT: A 106 ASP cc_start: 0.9310 (m-30) cc_final: 0.8926 (m-30) REVERT: D 34 LYS cc_start: 0.9267 (mmmm) cc_final: 0.8991 (mppt) REVERT: D 35 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8236 (mm-30) REVERT: D 42 TYR cc_start: 0.8789 (t80) cc_final: 0.8378 (t80) REVERT: D 56 SER cc_start: 0.9515 (OUTLIER) cc_final: 0.9205 (p) REVERT: D 108 LYS cc_start: 0.9211 (mtpp) cc_final: 0.9001 (mtpm) REVERT: E 59 GLU cc_start: 0.8907 (pm20) cc_final: 0.8580 (pm20) REVERT: E 129 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8193 (tmm160) REVERT: F 24 ASP cc_start: 0.8594 (t0) cc_final: 0.7992 (p0) REVERT: F 92 ARG cc_start: 0.9269 (OUTLIER) cc_final: 0.8950 (mtp85) REVERT: G 15 LYS cc_start: 0.9236 (ttmm) cc_final: 0.8902 (ttpp) REVERT: G 92 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8321 (mt-10) REVERT: H 35 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8070 (mm-30) REVERT: H 42 TYR cc_start: 0.8697 (t80) cc_final: 0.8360 (t80) REVERT: H 68 ASP cc_start: 0.9292 (t0) cc_final: 0.8960 (t0) REVERT: H 93 GLU cc_start: 0.9196 (mp0) cc_final: 0.8982 (mp0) REVERT: O 12 LYS cc_start: 0.9282 (ttmt) cc_final: 0.8957 (mtpt) REVERT: O 20 LYS cc_start: 0.9318 (ptmt) cc_final: 0.9069 (pptt) REVERT: O 40 GLU cc_start: 0.9571 (tp30) cc_final: 0.9295 (tp30) REVERT: M 91 LYS cc_start: 0.6979 (pttp) cc_final: 0.6697 (pptt) REVERT: N 30 ASP cc_start: 0.9025 (m-30) cc_final: 0.8793 (t0) REVERT: N 44 MET cc_start: 0.8917 (mmt) cc_final: 0.8588 (mmt) outliers start: 25 outliers final: 7 residues processed: 256 average time/residue: 0.8143 time to fit residues: 222.2086 Evaluate side-chains 241 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 230 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 116 LEU Chi-restraints excluded: chain D residue 56 SER 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 110 ASN Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain N residue 16 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 120 optimal weight: 30.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN G 24 GLN G 112 GLN O 44 GLN M 11 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 = 0.3581 r_free = 0.3581 target = 0.083003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.050942 restraints weight = 42535.620| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.70 r_work: 0.2644 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 15256 Z= 0.204 Angle : 0.597 10.122 21832 Z= 0.338 Chirality : 0.035 0.342 2461 Planarity : 0.004 0.042 1752 Dihedral : 30.222 97.775 4362 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.84 % Allowed : 22.01 % Favored : 74.15 % 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: 2.65 (0.26), residues: 1021 helix: 2.69 (0.19), residues: 725 sheet: -3.14 (1.60), residues: 10 loop : -0.61 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 33 TYR 0.010 0.001 TYR D 40 PHE 0.017 0.001 PHE N 22 TRP 0.010 0.002 TRP O 70 HIS 0.002 0.001 HIS N 10 Details of bonding type rmsd covalent geometry : bond 0.00456 (15256) covalent geometry : angle 0.59676 (21832) hydrogen bonds : bond 0.03885 ( 928) hydrogen bonds : angle 2.99415 ( 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 276 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 242 time to evaluate : 0.445 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: 0.9216 (OUTLIER) cc_final: 0.8925 (ptp-110) REVERT: A 56 LYS cc_start: 0.9450 (ttpp) cc_final: 0.9234 (ttmm) REVERT: A 59 GLU cc_start: 0.8460 (pm20) cc_final: 0.8152 (pm20) REVERT: A 120 MET cc_start: 0.8530 (mtt) cc_final: 0.8197 (mtt) REVERT: D 35 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8204 (mm-30) REVERT: D 42 TYR cc_start: 0.8815 (t80) cc_final: 0.8472 (t80) REVERT: D 56 SER cc_start: 0.9524 (OUTLIER) cc_final: 0.9198 (p) REVERT: D 105 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8456 (mt-10) REVERT: E 59 GLU cc_start: 0.9033 (pm20) cc_final: 0.8645 (pm20) REVERT: E 129 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8189 (tmm160) REVERT: F 92 ARG cc_start: 0.9291 (OUTLIER) cc_final: 0.8985 (mtp85) REVERT: F 93 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8876 (mm110) REVERT: G 15 LYS cc_start: 0.9218 (ttmm) cc_final: 0.8901 (ttpp) REVERT: G 92 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8348 (mt-10) REVERT: G 99 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8792 (mtpp) REVERT: H 33 ARG cc_start: 0.8203 (ttm110) cc_final: 0.7501 (mtp-110) REVERT: O 12 LYS cc_start: 0.9303 (ttmt) cc_final: 0.8986 (mtpt) REVERT: O 20 LYS cc_start: 0.9336 (ptmt) cc_final: 0.9082 (pptt) REVERT: O 40 GLU cc_start: 0.9650 (tp30) cc_final: 0.9423 (tp30) REVERT: M 91 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6737 (pptt) REVERT: N 44 MET cc_start: 0.8971 (mmt) cc_final: 0.8582 (mmt) outliers start: 34 outliers final: 11 residues processed: 259 average time/residue: 0.8389 time to fit residues: 231.5697 Evaluate side-chains 250 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 C residue 116 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 80 THR 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 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 91 LYS 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: 6.9990 chunk 24 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.082048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.050073 restraints weight = 42617.836| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.71 r_work: 0.2636 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15256 Z= 0.234 Angle : 0.618 10.635 21832 Z= 0.348 Chirality : 0.036 0.341 2461 Planarity : 0.004 0.043 1752 Dihedral : 30.352 96.131 4362 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.39 % Allowed : 23.48 % 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: 2.63 (0.19), residues: 725 sheet: -3.53 (1.56), residues: 10 loop : -0.68 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 67 TYR 0.010 0.001 TYR D 40 PHE 0.010 0.001 PHE A 67 TRP 0.006 0.001 TRP N 33 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00528 (15256) covalent geometry : angle 0.61789 (21832) hydrogen bonds : bond 0.04059 ( 928) hydrogen bonds : angle 3.03175 ( 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 268 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 238 time to evaluate : 0.288 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: A 42 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8853 (ptp-110) REVERT: A 56 LYS cc_start: 0.9448 (ttpp) cc_final: 0.9234 (ttmm) REVERT: A 59 GLU cc_start: 0.8496 (pm20) cc_final: 0.8153 (pm20) REVERT: A 106 ASP cc_start: 0.9328 (m-30) cc_final: 0.8982 (m-30) REVERT: A 120 MET cc_start: 0.8464 (mtt) cc_final: 0.8156 (mtt) REVERT: D 34 LYS cc_start: 0.9165 (mmmm) cc_final: 0.8878 (mppt) REVERT: D 35 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8145 (mm-30) REVERT: D 42 TYR cc_start: 0.8807 (t80) cc_final: 0.8464 (t80) REVERT: D 92 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8576 (ttp80) REVERT: D 105 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8323 (mt-10) REVERT: E 59 GLU cc_start: 0.9061 (pm20) cc_final: 0.8633 (pm20) REVERT: E 129 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8215 (tmm160) REVERT: F 92 ARG cc_start: 0.9301 (OUTLIER) cc_final: 0.9009 (mtp85) REVERT: F 93 GLN cc_start: 0.9133 (mm-40) cc_final: 0.8834 (mm110) REVERT: G 15 LYS cc_start: 0.9178 (ttmm) cc_final: 0.8906 (ttpp) REVERT: G 92 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8425 (mt-10) REVERT: G 99 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8746 (mtpp) REVERT: H 33 ARG cc_start: 0.8143 (ttm110) cc_final: 0.7516 (mtp-110) REVERT: H 35 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8108 (mm-30) REVERT: H 68 ASP cc_start: 0.9343 (t0) cc_final: 0.8990 (t0) REVERT: H 93 GLU cc_start: 0.9114 (mp0) cc_final: 0.8449 (mp0) REVERT: O 12 LYS cc_start: 0.9308 (ttmt) cc_final: 0.8974 (mtpt) REVERT: O 20 LYS cc_start: 0.9325 (ptmt) cc_final: 0.9092 (pptt) REVERT: O 40 GLU cc_start: 0.9650 (tp30) cc_final: 0.9389 (tp30) REVERT: M 120 LYS cc_start: 0.9534 (ptpt) cc_final: 0.9286 (pttt) REVERT: N 44 MET cc_start: 0.9084 (mmt) cc_final: 0.8659 (mmt) outliers start: 30 outliers final: 11 residues processed: 254 average time/residue: 0.7886 time to fit residues: 213.5411 Evaluate side-chains 248 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 232 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 C residue 116 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 80 THR 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 15 SER Chi-restraints excluded: chain N residue 16 ASP 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: 2.9990 chunk 12 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 125 optimal weight: 10.0000 chunk 104 optimal weight: 0.0050 chunk 17 optimal weight: 0.0980 chunk 126 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN F 27 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 = 0.3577 r_free = 0.3577 target = 0.082710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.050955 restraints weight = 42628.940| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.72 r_work: 0.2646 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15256 Z= 0.181 Angle : 0.621 11.205 21832 Z= 0.346 Chirality : 0.035 0.346 2461 Planarity : 0.004 0.041 1752 Dihedral : 30.318 96.425 4362 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.93 % Allowed : 24.83 % Favored : 72.23 % 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: 2.58 (0.26), residues: 1021 helix: 2.65 (0.19), residues: 725 sheet: -3.62 (1.56), residues: 10 loop : -0.65 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 132 TYR 0.011 0.001 TYR D 37 PHE 0.016 0.001 PHE M 58 TRP 0.008 0.001 TRP N 33 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00406 (15256) covalent geometry : angle 0.62100 (21832) hydrogen bonds : bond 0.03715 ( 928) hydrogen bonds : angle 2.99007 ( 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 269 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 0.433 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: A 42 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8925 (ptp-110) REVERT: A 56 LYS cc_start: 0.9446 (ttpp) cc_final: 0.9246 (ttmm) REVERT: A 59 GLU cc_start: 0.8505 (pm20) cc_final: 0.8171 (pm20) REVERT: C 116 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9161 (mm) REVERT: D 34 LYS cc_start: 0.9197 (mmmm) cc_final: 0.8773 (mmtm) REVERT: D 35 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8205 (mm-30) REVERT: D 42 TYR cc_start: 0.8810 (t80) cc_final: 0.8468 (t80) REVERT: D 105 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8380 (mt-10) REVERT: E 59 GLU cc_start: 0.9069 (pm20) cc_final: 0.8701 (pm20) REVERT: E 129 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8204 (tmm160) REVERT: F 92 ARG cc_start: 0.9281 (OUTLIER) cc_final: 0.8940 (mtp85) REVERT: F 93 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8843 (mm110) REVERT: G 15 LYS cc_start: 0.9210 (ttmm) cc_final: 0.8944 (ttpp) REVERT: G 92 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8432 (mt-10) REVERT: G 99 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8747 (mtpp) REVERT: H 33 ARG cc_start: 0.8162 (ttm110) cc_final: 0.7489 (mtp-110) REVERT: H 68 ASP cc_start: 0.9314 (t0) cc_final: 0.8957 (t0) REVERT: H 93 GLU cc_start: 0.9096 (mp0) cc_final: 0.8463 (mp0) REVERT: O 12 LYS cc_start: 0.9308 (ttmt) cc_final: 0.9019 (mtpt) REVERT: O 20 LYS cc_start: 0.9345 (ptmt) cc_final: 0.9103 (pptt) REVERT: O 40 GLU cc_start: 0.9641 (tp30) cc_final: 0.9412 (tp30) REVERT: M 38 MET cc_start: 0.8651 (mpm) cc_final: 0.8086 (mpp) REVERT: M 91 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6767 (pptt) REVERT: M 120 LYS cc_start: 0.9568 (ptpt) cc_final: 0.9182 (pttm) REVERT: N 44 MET cc_start: 0.9111 (mmt) cc_final: 0.8676 (mmt) outliers start: 26 outliers final: 9 residues processed: 256 average time/residue: 0.8071 time to fit residues: 220.3924 Evaluate side-chains 243 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 228 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 C residue 116 LEU Chi-restraints excluded: chain D residue 68 ASP 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 15 SER Chi-restraints excluded: chain M residue 91 LYS Chi-restraints excluded: chain N residue 16 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 87 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 124 optimal weight: 0.0370 chunk 1 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 112 GLN G 24 GLN ** M 118 ASN ** 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 = 0.3560 r_free = 0.3560 target = 0.081772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.049927 restraints weight = 42566.347| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.69 r_work: 0.2631 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 15256 Z= 0.234 Angle : 0.623 11.259 21832 Z= 0.351 Chirality : 0.036 0.361 2461 Planarity : 0.004 0.047 1752 Dihedral : 30.388 97.730 4362 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.60 % Allowed : 26.41 % Favored : 70.99 % 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: 2.51 (0.26), residues: 1021 helix: 2.61 (0.19), residues: 726 sheet: -3.70 (1.56), residues: 10 loop : -0.73 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG M 37 TYR 0.014 0.001 TYR E 99 PHE 0.012 0.001 PHE M 124 TRP 0.009 0.001 TRP N 33 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00528 (15256) covalent geometry : angle 0.62298 (21832) hydrogen bonds : bond 0.04118 ( 928) hydrogen bonds : angle 3.04727 ( 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 257 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 0.304 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: 0.9164 (OUTLIER) cc_final: 0.8847 (ptp-110) REVERT: A 56 LYS cc_start: 0.9442 (ttpp) cc_final: 0.9238 (ttmm) REVERT: A 59 GLU cc_start: 0.8531 (pm20) cc_final: 0.8161 (pm20) REVERT: A 106 ASP cc_start: 0.9331 (m-30) cc_final: 0.8976 (m-30) REVERT: D 35 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8200 (mm-30) REVERT: D 42 TYR cc_start: 0.8821 (t80) cc_final: 0.8483 (t80) REVERT: D 105 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8431 (mt-10) REVERT: E 59 GLU cc_start: 0.9085 (pm20) cc_final: 0.8660 (pm20) REVERT: E 129 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8247 (tmm160) REVERT: F 24 ASP cc_start: 0.8370 (t0) cc_final: 0.7466 (p0) REVERT: F 92 ARG cc_start: 0.9300 (OUTLIER) cc_final: 0.9009 (mtp85) REVERT: F 93 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8829 (mm110) REVERT: G 15 LYS cc_start: 0.9180 (ttmm) cc_final: 0.8890 (ttpp) REVERT: G 92 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8416 (mt-10) REVERT: G 99 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8735 (mtpp) REVERT: H 35 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8654 (mm-30) REVERT: H 68 ASP cc_start: 0.9355 (t0) cc_final: 0.8974 (t0) REVERT: H 93 GLU cc_start: 0.9121 (mp0) cc_final: 0.8912 (mp0) REVERT: O 12 LYS cc_start: 0.9315 (ttmt) cc_final: 0.8989 (mtpt) REVERT: O 20 LYS cc_start: 0.9321 (ptmt) cc_final: 0.9109 (pptt) REVERT: O 35 ARG cc_start: 0.9452 (tpp80) cc_final: 0.9120 (tpp80) REVERT: M 91 LYS cc_start: 0.7011 (pttp) cc_final: 0.6690 (pptt) REVERT: M 120 LYS cc_start: 0.9573 (ptpt) cc_final: 0.9359 (pttm) REVERT: N 44 MET cc_start: 0.9153 (mmt) cc_final: 0.8714 (mmt) outliers start: 23 outliers final: 12 residues processed: 246 average time/residue: 0.8455 time to fit residues: 221.3860 Evaluate side-chains 243 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 227 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 C residue 116 LEU Chi-restraints excluded: chain D residue 52 THR 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 15 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 112 optimal weight: 0.5980 chunk 69 optimal weight: 0.0670 chunk 118 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 66 optimal weight: 0.0870 chunk 33 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 112 GLN F 27 GLN G 112 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 = 0.3597 r_free = 0.3597 target = 0.083638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.051906 restraints weight = 42053.752| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.71 r_work: 0.2686 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15256 Z= 0.150 Angle : 0.662 13.061 21832 Z= 0.362 Chirality : 0.035 0.361 2461 Planarity : 0.004 0.054 1752 Dihedral : 30.293 98.366 4362 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.03 % Allowed : 27.77 % Favored : 70.20 % 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: 2.51 (0.26), residues: 1021 helix: 2.61 (0.19), residues: 726 sheet: -3.74 (1.55), residues: 10 loop : -0.71 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG O 30 TYR 0.013 0.001 TYR D 37 PHE 0.013 0.001 PHE M 61 TRP 0.015 0.002 TRP N 33 HIS 0.004 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00326 (15256) covalent geometry : angle 0.66171 (21832) hydrogen bonds : bond 0.03581 ( 928) hydrogen bonds : angle 3.02022 ( 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 265 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 0.447 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: A 56 LYS cc_start: 0.9439 (ttpp) cc_final: 0.9239 (ttmm) REVERT: A 59 GLU cc_start: 0.8452 (pm20) cc_final: 0.8113 (pm20) REVERT: C 116 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9114 (mm) REVERT: D 35 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8197 (mm-30) REVERT: D 105 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8421 (mt-10) REVERT: E 59 GLU cc_start: 0.9079 (pm20) cc_final: 0.8710 (pm20) REVERT: E 129 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8204 (tmm160) REVERT: F 24 ASP cc_start: 0.8406 (t0) cc_final: 0.7473 (p0) REVERT: F 92 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8921 (mtp85) REVERT: F 93 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8810 (mm110) REVERT: G 15 LYS cc_start: 0.9161 (ttmm) cc_final: 0.8816 (ttpp) REVERT: G 92 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8358 (mt-10) REVERT: H 33 ARG cc_start: 0.8051 (ttm110) cc_final: 0.7503 (mtp-110) REVERT: H 35 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8677 (mm-30) REVERT: H 68 ASP cc_start: 0.9355 (t0) cc_final: 0.8998 (t0) REVERT: H 93 GLU cc_start: 0.9096 (mp0) cc_final: 0.8488 (mp0) REVERT: O 12 LYS cc_start: 0.9269 (ttmt) cc_final: 0.9002 (mtpt) REVERT: O 20 LYS cc_start: 0.9306 (ptmt) cc_final: 0.9049 (pptt) REVERT: O 40 GLU cc_start: 0.9641 (tp30) cc_final: 0.9378 (tp30) REVERT: M 91 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6731 (pptt) REVERT: M 116 GLU cc_start: 0.9674 (mm-30) cc_final: 0.9018 (pt0) REVERT: M 120 LYS cc_start: 0.9572 (ptpt) cc_final: 0.9247 (pttp) REVERT: M 133 ARG cc_start: 0.9419 (tpm170) cc_final: 0.9182 (tpm170) REVERT: N 44 MET cc_start: 0.9204 (mmt) cc_final: 0.8746 (mmt) outliers start: 18 outliers final: 9 residues processed: 257 average time/residue: 0.8398 time to fit residues: 230.1071 Evaluate side-chains 249 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 236 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 76 GLN 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 110 ASN Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain M residue 91 LYS 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: 0.9990 chunk 114 optimal weight: 0.0070 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 113 optimal weight: 0.0980 chunk 91 optimal weight: 7.9990 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 112 GLN G 112 GLN M 56 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 = 0.3618 r_free = 0.3618 target = 0.084501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.052869 restraints weight = 42254.216| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.70 r_work: 0.2714 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2726 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= 0.151 Angle : 0.661 16.968 21832 Z= 0.360 Chirality : 0.035 0.363 2461 Planarity : 0.004 0.048 1752 Dihedral : 30.079 99.311 4362 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.92 % Allowed : 28.22 % 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: 2.57 (0.26), residues: 1021 helix: 2.66 (0.19), residues: 725 sheet: -3.87 (1.60), residues: 10 loop : -0.66 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG O 30 TYR 0.014 0.001 TYR F 88 PHE 0.010 0.001 PHE E 67 TRP 0.019 0.002 TRP O 70 HIS 0.004 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00331 (15256) covalent geometry : angle 0.66054 (21832) hydrogen bonds : bond 0.03620 ( 928) hydrogen bonds : angle 3.04744 ( 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 266 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 249 time to evaluate : 0.297 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 59 GLU cc_start: 0.8389 (pm20) cc_final: 0.8113 (pm20) REVERT: C 116 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9075 (mm) REVERT: D 34 LYS cc_start: 0.9173 (mmmm) cc_final: 0.8821 (mptt) REVERT: D 35 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8185 (mm-30) REVERT: D 105 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8442 (mt-10) REVERT: E 59 GLU cc_start: 0.9089 (pm20) cc_final: 0.8664 (pm20) REVERT: E 129 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8209 (tmm160) REVERT: F 24 ASP cc_start: 0.8431 (t0) cc_final: 0.7505 (p0) REVERT: F 92 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8920 (mtp85) REVERT: F 93 GLN cc_start: 0.9107 (mm-40) cc_final: 0.8737 (mm110) REVERT: G 15 LYS cc_start: 0.9158 (ttmm) cc_final: 0.8806 (ttpp) REVERT: G 92 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8364 (mt-10) REVERT: H 33 ARG cc_start: 0.7928 (ttm110) cc_final: 0.7496 (mtp-110) REVERT: H 35 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8640 (mm-30) REVERT: H 68 ASP cc_start: 0.9359 (t0) cc_final: 0.9006 (t0) REVERT: H 93 GLU cc_start: 0.9097 (mp0) cc_final: 0.8480 (mp0) REVERT: O 20 LYS cc_start: 0.9313 (ptmt) cc_final: 0.9045 (pptt) REVERT: M 38 MET cc_start: 0.8668 (mpm) cc_final: 0.8042 (mpp) REVERT: M 91 LYS cc_start: 0.6983 (OUTLIER) cc_final: 0.6674 (pptt) REVERT: M 115 LYS cc_start: 0.9484 (mtpp) cc_final: 0.9278 (ptpp) REVERT: M 116 GLU cc_start: 0.9617 (mm-30) cc_final: 0.9107 (pt0) REVERT: M 120 LYS cc_start: 0.9454 (ptpt) cc_final: 0.9130 (pttp) REVERT: M 132 ARG cc_start: 0.8912 (ttp80) cc_final: 0.8524 (tmm160) REVERT: N 44 MET cc_start: 0.9192 (mmt) cc_final: 0.8737 (mmt) outliers start: 17 outliers final: 8 residues processed: 258 average time/residue: 0.7858 time to fit residues: 216.3946 Evaluate side-chains 251 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 239 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 116 LEU Chi-restraints excluded: chain D residue 100 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 O residue 15 SER Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain M residue 91 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN F 27 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 = 0.3605 r_free = 0.3605 target = 0.083898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.052363 restraints weight = 42265.488| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.68 r_work: 0.2688 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15256 Z= 0.176 Angle : 0.694 19.934 21832 Z= 0.373 Chirality : 0.036 0.361 2461 Planarity : 0.004 0.046 1752 Dihedral : 30.124 100.458 4362 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.58 % Allowed : 29.68 % Favored : 68.74 % 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: 2.57 (0.26), residues: 1021 helix: 2.65 (0.19), residues: 726 sheet: -4.14 (1.60), residues: 10 loop : -0.63 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 132 TYR 0.021 0.001 TYR F 88 PHE 0.008 0.001 PHE E 67 TRP 0.016 0.002 TRP O 70 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00393 (15256) covalent geometry : angle 0.69376 (21832) hydrogen bonds : bond 0.03732 ( 928) hydrogen bonds : angle 3.09532 ( 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 252 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 0.276 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: 0.8435 (pm20) cc_final: 0.8135 (pm20) REVERT: C 116 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9148 (mm) REVERT: D 34 LYS cc_start: 0.9194 (mmmm) cc_final: 0.8838 (mptt) REVERT: D 35 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8166 (mm-30) REVERT: D 105 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8498 (mt-10) REVERT: E 59 GLU cc_start: 0.9107 (pm20) cc_final: 0.8761 (pm20) REVERT: E 129 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8185 (tmm160) REVERT: F 92 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8952 (mtp85) REVERT: F 93 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8757 (mm110) REVERT: G 15 LYS cc_start: 0.9200 (ttmm) cc_final: 0.8880 (ttpp) REVERT: G 92 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8383 (mt-10) REVERT: G 99 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8721 (mtpp) REVERT: H 33 ARG cc_start: 0.7932 (ttm110) cc_final: 0.7423 (mtp-110) REVERT: H 35 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8587 (mm-30) REVERT: H 68 ASP cc_start: 0.9335 (t0) cc_final: 0.8995 (t0) REVERT: H 93 GLU cc_start: 0.9081 (mp0) cc_final: 0.8466 (mp0) REVERT: O 20 LYS cc_start: 0.9311 (ptmt) cc_final: 0.9088 (pptt) REVERT: M 37 ARG cc_start: 0.8534 (mmm160) cc_final: 0.8087 (mmm160) REVERT: M 91 LYS cc_start: 0.6963 (pttp) cc_final: 0.6654 (pptt) REVERT: M 120 LYS cc_start: 0.9512 (ptpt) cc_final: 0.9137 (pttp) REVERT: M 132 ARG cc_start: 0.8832 (ttp80) cc_final: 0.8619 (tmm160) REVERT: N 26 MET cc_start: 0.8187 (tmm) cc_final: 0.7912 (tmm) REVERT: N 44 MET cc_start: 0.9172 (mmt) cc_final: 0.8733 (mmt) outliers start: 14 outliers final: 9 residues processed: 247 average time/residue: 0.8458 time to fit residues: 222.4392 Evaluate side-chains 245 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 232 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 116 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 100 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 M residue 58 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 46 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 0.0470 chunk 16 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN O 14 ASN ** 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 = 0.3627 r_free = 0.3627 target = 0.084932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.053124 restraints weight = 42629.353| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.72 r_work: 0.2720 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15256 Z= 0.155 Angle : 0.705 20.856 21832 Z= 0.377 Chirality : 0.036 0.353 2461 Planarity : 0.004 0.044 1752 Dihedral : 30.048 100.969 4362 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.35 % Allowed : 30.25 % Favored : 68.40 % 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: 2.58 (0.26), residues: 1021 helix: 2.64 (0.19), residues: 725 sheet: -3.88 (1.72), residues: 10 loop : -0.62 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 132 TYR 0.018 0.001 TYR D 40 PHE 0.011 0.001 PHE M 61 TRP 0.017 0.002 TRP O 70 HIS 0.005 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00344 (15256) covalent geometry : angle 0.70484 (21832) hydrogen bonds : bond 0.03566 ( 928) hydrogen bonds : angle 3.10948 ( 2371) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6164.21 seconds wall clock time: 105 minutes 25.73 seconds (6325.73 seconds total)