Starting phenix.real_space_refine on Sat Jul 4 02:10:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w74_65716/07_2026/9w74_65716.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w74_65716/07_2026/9w74_65716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w74_65716/07_2026/9w74_65716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w74_65716/07_2026/9w74_65716.map" model { file = "/net/cci-nas-00/data/ceres_data/9w74_65716/07_2026/9w74_65716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w74_65716/07_2026/9w74_65716.cif" } resolution = 4.94 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= 0.002 sd= 0.043 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 412 5.49 5 S 20 5.16 5 C 9679 2.51 5 N 3130 2.21 5 O 4022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17263 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 740 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 618 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "K" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "L" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "M" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "N" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "O" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "P" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 618 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "I" Number of atoms: 4344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 4344 Classifications: {'DNA': 207} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 206} Chain: "J" Number of atoms: 4137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 4137 Classifications: {'DNA': 207} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 206} Time building chain proxies: 2.92, per 1000 atoms: 0.17 Number of scatterers: 17263 At special positions: 0 Unit cell: (103.88, 119.78, 150.52, 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 20 16.00 P 412 15.00 O 4022 8.00 N 3130 7.00 C 9679 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: 1.28 Conformation dependent library (CDL) restraints added in 450.8 milliseconds 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 8 sheets defined 73.6% alpha, 1.5% beta 201 base pairs and 382 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 removed outlier: 4.253A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.706A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.701A pdb=" N ILE B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 50 through 77 Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.718A pdb=" N ASN C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.463A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.670A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.685A pdb=" N LEU C 116 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 4.278A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.920A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.770A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 47 through 76 removed outlier: 4.228A pdb=" N TYR F 51 " --> pdb=" O SER F 47 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'K' and resid 44 through 56 Processing helix chain 'K' and resid 63 through 79 Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 removed outlier: 3.539A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 29 removed outlier: 3.884A pdb=" N GLN L 27 " --> pdb=" O ASP L 24 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE L 29 " --> pdb=" O ILE L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 76 removed outlier: 3.822A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 Processing helix chain 'M' and resid 17 through 22 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.226A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 90 Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'N' and resid 34 through 46 Processing helix chain 'N' and resid 52 through 81 Processing helix chain 'N' and resid 87 through 99 removed outlier: 3.603A pdb=" N ILE N 91 " --> pdb=" O THR N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 121 Processing helix chain 'O' and resid 44 through 57 Processing helix chain 'O' and resid 63 through 76 removed outlier: 3.617A pdb=" N PHE O 67 " --> pdb=" O ARG O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 121 through 132 Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 47 through 75 removed outlier: 3.924A pdb=" N TYR P 51 " --> pdb=" O SER P 47 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU P 52 " --> pdb=" O GLY P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 93 Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.553A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA3, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'K' and resid 83 through 84 Processing sheet with id=AA5, first strand: chain 'K' and resid 118 through 119 removed outlier: 7.089A pdb=" N ARG L 45 " --> pdb=" O ILE K 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.924A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'M' and resid 100 through 101 Processing sheet with id=AA8, first strand: chain 'O' and resid 118 through 119 594 hydrogen bonds defined for protein. 1773 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 402 hydrogen bonds 804 hydrogen bond angles 0 basepair planarities 201 basepair parallelities 382 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2790 1.33 - 1.45: 6256 1.45 - 1.57: 8502 1.57 - 1.69: 824 1.69 - 1.81: 36 Bond restraints: 18408 Sorted by residual: bond pdb=" C3' DA I 173 " pdb=" C2' DA I 173 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.54e+01 bond pdb=" C3' DA I 172 " pdb=" O3' DA I 172 " ideal model delta sigma weight residual 1.435 1.387 0.048 1.30e-02 5.92e+03 1.35e+01 bond pdb=" C3' DT J -28 " pdb=" O3' DT J -28 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.23e+01 bond pdb=" C3' DT J -50 " pdb=" C2' DT J -50 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C3' DA I 7 " pdb=" O3' DA I 7 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.20e+01 ... (remaining 18403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 24246 1.68 - 3.35: 2234 3.35 - 5.03: 121 5.03 - 6.70: 24 6.70 - 8.38: 3 Bond angle restraints: 26628 Sorted by residual: angle pdb=" O4' DT J-145 " pdb=" C4' DT J-145 " pdb=" C3' DT J-145 " ideal model delta sigma weight residual 106.00 102.63 3.37 6.00e-01 2.78e+00 3.16e+01 angle pdb=" O4' DT J -72 " pdb=" C4' DT J -72 " pdb=" C3' DT J -72 " ideal model delta sigma weight residual 106.00 102.73 3.27 6.00e-01 2.78e+00 2.97e+01 angle pdb=" O4' DT J-144 " pdb=" C4' DT J-144 " pdb=" C3' DT J-144 " ideal model delta sigma weight residual 106.00 102.74 3.26 6.00e-01 2.78e+00 2.95e+01 angle pdb=" O4' DT J-118 " pdb=" C4' DT J-118 " pdb=" C3' DT J-118 " ideal model delta sigma weight residual 106.00 103.09 2.91 6.00e-01 2.78e+00 2.35e+01 angle pdb=" O4' DT J -71 " pdb=" C4' DT J -71 " pdb=" C3' DT J -71 " ideal model delta sigma weight residual 106.00 103.11 2.89 6.00e-01 2.78e+00 2.32e+01 ... (remaining 26623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.59: 8166 34.59 - 69.18: 2211 69.18 - 103.76: 102 103.76 - 138.35: 1 138.35 - 172.94: 2 Dihedral angle restraints: 10482 sinusoidal: 7292 harmonic: 3190 Sorted by residual: dihedral pdb=" CA GLN P 27 " pdb=" C GLN P 27 " pdb=" N GLY P 28 " pdb=" CA GLY P 28 " ideal model delta harmonic sigma weight residual 180.00 157.36 22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA LYS E 64 " pdb=" C LYS E 64 " pdb=" N LEU E 65 " pdb=" CA LEU E 65 " ideal model delta harmonic sigma weight residual 180.00 -159.05 -20.95 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ARG B 23 " pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 10479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1911 0.040 - 0.080: 822 0.080 - 0.121: 243 0.121 - 0.161: 51 0.161 - 0.201: 5 Chirality restraints: 3032 Sorted by residual: chirality pdb=" CB ILE E 130 " pdb=" CA ILE E 130 " pdb=" CG1 ILE E 130 " pdb=" CG2 ILE E 130 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLU A 105 " pdb=" N GLU A 105 " pdb=" C GLU A 105 " pdb=" CB GLU A 105 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" C3' DT J -86 " pdb=" C4' DT J -86 " pdb=" O3' DT J -86 " pdb=" C2' DT J -86 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 3029 not shown) Planarity restraints: 1934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE M 79 " -0.044 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO M 80 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO M 80 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO M 80 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 104 " -0.014 2.00e-02 2.50e+03 1.82e-02 5.82e+00 pdb=" CG PHE K 104 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE K 104 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE K 104 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE K 104 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE K 104 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE K 104 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 93 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C GLN A 93 " -0.037 2.00e-02 2.50e+03 pdb=" O GLN A 93 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU A 94 " 0.012 2.00e-02 2.50e+03 ... (remaining 1931 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 4976 2.83 - 3.35: 19590 3.35 - 3.87: 37317 3.87 - 4.38: 41860 4.38 - 4.90: 55004 Nonbonded interactions: 158747 Sorted by model distance: nonbonded pdb=" O HIS D 106 " pdb=" OE1 GLU D 110 " model vdw 2.317 3.040 nonbonded pdb=" O VAL A 101 " pdb=" OE1 GLU A 105 " model vdw 2.367 3.040 nonbonded pdb=" O GLN A 93 " pdb=" OE1 GLU A 97 " model vdw 2.370 3.040 nonbonded pdb=" O MET K 90 " pdb=" OE1 GLU K 94 " model vdw 2.373 3.040 nonbonded pdb=" O VAL K 101 " pdb=" OE1 GLU K 105 " model vdw 2.386 3.040 ... (remaining 158742 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 45 through 134) selection = (chain 'K' and resid 45 through 134) selection = (chain 'O' and resid 45 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' selection = (chain 'L' and resid 25 through 102) selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.290 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.970 Find NCS groups from input model: 0.190 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: 0.020 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.007 0.048 18408 Z= 0.623 Angle : 0.918 8.380 26628 Z= 0.821 Chirality : 0.048 0.201 3032 Planarity : 0.006 0.067 1934 Dihedral : 29.700 172.938 8422 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 27.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: -0.10 (0.24), residues: 1075 helix: 0.51 (0.18), residues: 773 sheet: None (None), residues: 0 loop : -1.40 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 83 TYR 0.022 0.002 TYR A 54 PHE 0.042 0.003 PHE K 104 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.62 (18408) covalent geometry : angle 0.91768 / 0.82 (26628) hydrogen bonds : bond 0.12102 / 8.07 ( 996) hydrogen bonds : angle 5.48595 / 4.02 ( 2577) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.435 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: symmetry clash REVERT: A 120 MET cc_start: 0.9334 (tpt) cc_final: 0.9093 (mmm) REVERT: A 130 ILE cc_start: 0.9515 (mp) cc_final: 0.8525 (mp) REVERT: D 65 ASP cc_start: 0.9757 (t0) cc_final: 0.9420 (t0) REVERT: D 69 ARG cc_start: 0.9196 (mtp180) cc_final: 0.8778 (ptp-170) REVERT: E 67 PHE cc_start: 0.8809 (t80) cc_final: 0.8405 (t80) REVERT: E 106 ASP cc_start: 0.9304 (m-30) cc_final: 0.9075 (m-30) REVERT: E 129 ARG cc_start: 0.9721 (tpp-160) cc_final: 0.9417 (tmm160) REVERT: F 44 LYS cc_start: 0.9476 (mtmt) cc_final: 0.9271 (tmtt) REVERT: F 61 PHE cc_start: 0.9156 (t80) cc_final: 0.8913 (t80) REVERT: K 55 GLN cc_start: 0.7702 (tp40) cc_final: 0.7236 (mm110) REVERT: K 108 ASN cc_start: 0.8222 (t0) cc_final: 0.7988 (m-40) REVERT: M 95 LYS cc_start: 0.9500 (tppt) cc_final: 0.9247 (tmmt) REVERT: N 56 MET cc_start: 0.9520 (ptp) cc_final: 0.9275 (mpp) REVERT: N 110 GLU cc_start: 0.9384 (mm-30) cc_final: 0.8948 (tp30) REVERT: O 93 GLN cc_start: 0.9736 (tp-100) cc_final: 0.9132 (tp-100) REVERT: O 97 GLU cc_start: 0.9774 (mt-10) cc_final: 0.9256 (mt-10) REVERT: P 59 LYS cc_start: 0.8837 (mttp) cc_final: 0.8478 (mmmt) REVERT: P 88 TYR cc_start: 0.9667 (t80) cc_final: 0.9219 (t80) REVERT: P 95 ARG cc_start: 0.9491 (mmp80) cc_final: 0.9291 (mmm160) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1274 time to fit residues: 35.1606 Evaluate side-chains 129 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 40.0000 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 40.0000 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 HIS O 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.045833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.034130 restraints weight = 249342.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.035136 restraints weight = 149911.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.035864 restraints weight = 104082.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.036417 restraints weight = 79356.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.036805 restraints weight = 63978.513| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18408 Z= 0.250 Angle : 0.817 9.310 26628 Z= 0.484 Chirality : 0.049 0.250 3032 Planarity : 0.006 0.064 1934 Dihedral : 33.236 167.967 6222 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 31.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.33 % Allowed : 7.28 % Favored : 92.39 % 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: -0.04 (0.24), residues: 1075 helix: 0.57 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -1.44 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG E 131 TYR 0.021 0.002 TYR P 72 PHE 0.036 0.003 PHE K 104 HIS 0.008 0.002 HIS N 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.25 (18408) covalent geometry : angle 0.81705 / 0.48 (26628) hydrogen bonds : bond 0.12517 / 8.42 ( 996) hydrogen bonds : angle 5.00508 / 3.64 ( 2577) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 175 time to evaluate : 0.435 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9640 (mp0) cc_final: 0.9365 (mp0) REVERT: C 64 GLU cc_start: 0.9259 (tp30) cc_final: 0.8894 (tp30) REVERT: E 67 PHE cc_start: 0.8994 (t80) cc_final: 0.8551 (t80) REVERT: F 44 LYS cc_start: 0.9582 (mtmt) cc_final: 0.9309 (tmtt) REVERT: F 61 PHE cc_start: 0.9306 (t80) cc_final: 0.9035 (t80) REVERT: K 55 GLN cc_start: 0.7694 (tp40) cc_final: 0.7263 (mm110) REVERT: K 108 ASN cc_start: 0.8204 (t0) cc_final: 0.7971 (m-40) REVERT: L 53 GLU cc_start: 0.9069 (tt0) cc_final: 0.8790 (tt0) REVERT: O 93 GLN cc_start: 0.9771 (tp-100) cc_final: 0.9306 (tm-30) REVERT: P 59 LYS cc_start: 0.8822 (mttp) cc_final: 0.8470 (mmmt) REVERT: P 88 TYR cc_start: 0.9637 (t80) cc_final: 0.9244 (t80) outliers start: 3 outliers final: 1 residues processed: 178 average time/residue: 0.1147 time to fit residues: 31.2517 Evaluate side-chains 122 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 125 optimal weight: 50.0000 chunk 112 optimal weight: 40.0000 chunk 43 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 127 optimal weight: 50.0000 chunk 12 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 113 optimal weight: 30.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 GLN ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 HIS O 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.047486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.035474 restraints weight = 243072.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.036581 restraints weight = 144682.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.037360 restraints weight = 99351.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.037930 restraints weight = 74944.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.038306 restraints weight = 60518.192| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 18408 Z= 0.178 Angle : 0.752 7.678 26628 Z= 0.451 Chirality : 0.048 0.230 3032 Planarity : 0.005 0.058 1934 Dihedral : 33.211 163.801 6222 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.33 % Allowed : 5.65 % Favored : 94.02 % 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: 0.13 (0.24), residues: 1075 helix: 0.70 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -1.37 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 32 TYR 0.031 0.002 TYR M 39 PHE 0.034 0.002 PHE K 104 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.18 (18408) covalent geometry : angle 0.75220 / 0.45 (26628) hydrogen bonds : bond 0.08621 / 5.88 ( 996) hydrogen bonds : angle 4.70724 / 3.41 ( 2577) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 184 time to evaluate : 0.312 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9336 (tpt) cc_final: 0.9077 (mmm) REVERT: C 64 GLU cc_start: 0.9179 (tp30) cc_final: 0.8691 (tp30) REVERT: D 69 ARG cc_start: 0.9184 (mtp180) cc_final: 0.8883 (ptm160) REVERT: E 67 PHE cc_start: 0.8854 (t80) cc_final: 0.8405 (t80) REVERT: E 103 LEU cc_start: 0.9427 (mm) cc_final: 0.9208 (mm) REVERT: E 129 ARG cc_start: 0.9714 (tpp-160) cc_final: 0.9479 (tmm160) REVERT: F 44 LYS cc_start: 0.9444 (mtmt) cc_final: 0.9221 (tmtt) REVERT: F 59 LYS cc_start: 0.9768 (tptp) cc_final: 0.9560 (tptp) REVERT: K 55 GLN cc_start: 0.7763 (tp40) cc_final: 0.7333 (mm110) REVERT: K 108 ASN cc_start: 0.8131 (t0) cc_final: 0.7850 (m-40) REVERT: L 53 GLU cc_start: 0.9040 (tt0) cc_final: 0.8746 (tt0) REVERT: M 104 GLN cc_start: 0.6656 (OUTLIER) cc_final: 0.6141 (pp30) REVERT: O 93 GLN cc_start: 0.9750 (tp-100) cc_final: 0.9285 (tm-30) REVERT: P 59 LYS cc_start: 0.8689 (mttp) cc_final: 0.8373 (mmmt) REVERT: P 88 TYR cc_start: 0.9636 (t80) cc_final: 0.9208 (t80) outliers start: 3 outliers final: 0 residues processed: 186 average time/residue: 0.1265 time to fit residues: 35.1737 Evaluate side-chains 130 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 50.0000 chunk 2 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 137 optimal weight: 30.0000 chunk 122 optimal weight: 50.0000 chunk 21 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 107 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 HIS O 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.045426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.033772 restraints weight = 251547.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.034780 restraints weight = 150382.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.035522 restraints weight = 104511.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.036059 restraints weight = 79111.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.036434 restraints weight = 64011.372| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18408 Z= 0.242 Angle : 0.803 8.859 26628 Z= 0.476 Chirality : 0.049 0.227 3032 Planarity : 0.006 0.055 1934 Dihedral : 33.304 162.822 6222 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 32.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % 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: -0.07 (0.24), residues: 1075 helix: 0.56 (0.18), residues: 770 sheet: None (None), residues: 0 loop : -1.47 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 92 TYR 0.029 0.002 TYR M 39 PHE 0.019 0.002 PHE K 67 HIS 0.011 0.002 HIS N 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.24 (18408) covalent geometry : angle 0.80347 / 0.48 (26628) hydrogen bonds : bond 0.13288 / 8.96 ( 996) hydrogen bonds : angle 4.98790 / 3.62 ( 2577) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.301 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.9277 (tp30) cc_final: 0.8805 (tp30) REVERT: D 69 ARG cc_start: 0.9218 (mtp180) cc_final: 0.9013 (ttm110) REVERT: E 67 PHE cc_start: 0.8853 (t80) cc_final: 0.8444 (t80) REVERT: K 55 GLN cc_start: 0.7797 (tp40) cc_final: 0.7340 (mm110) REVERT: K 108 ASN cc_start: 0.8210 (t0) cc_final: 0.8000 (m-40) REVERT: L 53 GLU cc_start: 0.9083 (tt0) cc_final: 0.8794 (tt0) REVERT: N 62 PHE cc_start: 0.9780 (t80) cc_final: 0.9578 (t80) REVERT: O 93 GLN cc_start: 0.9737 (tp-100) cc_final: 0.9247 (tm-30) REVERT: P 59 LYS cc_start: 0.8701 (mttp) cc_final: 0.8343 (mmmt) REVERT: P 88 TYR cc_start: 0.9656 (t80) cc_final: 0.9252 (t80) REVERT: P 98 TYR cc_start: 0.8487 (m-80) cc_final: 0.8124 (m-80) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1173 time to fit residues: 30.4223 Evaluate side-chains 123 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 115 optimal weight: 50.0000 chunk 38 optimal weight: 0.0270 chunk 83 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 HIS O 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.047637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.035690 restraints weight = 239309.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.036779 restraints weight = 143728.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.037564 restraints weight = 99106.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.038144 restraints weight = 74829.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.038539 restraints weight = 60034.912| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18408 Z= 0.164 Angle : 0.755 7.094 26628 Z= 0.449 Chirality : 0.047 0.232 3032 Planarity : 0.005 0.056 1934 Dihedral : 33.272 160.064 6222 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.11 % Allowed : 4.35 % Favored : 95.54 % 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: 0.18 (0.24), residues: 1075 helix: 0.74 (0.18), residues: 770 sheet: None (None), residues: 0 loop : -1.35 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 67 TYR 0.029 0.002 TYR M 39 PHE 0.033 0.002 PHE E 104 HIS 0.009 0.001 HIS N 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.16 (18408) covalent geometry : angle 0.75467 / 0.45 (26628) hydrogen bonds : bond 0.07884 / 5.42 ( 996) hydrogen bonds : angle 4.65929 / 3.36 ( 2577) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.411 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: 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 120 MET cc_start: 0.9286 (tpt) cc_final: 0.9025 (mmm) REVERT: C 64 GLU cc_start: 0.9220 (tp30) cc_final: 0.8800 (tp30) REVERT: E 67 PHE cc_start: 0.8839 (t80) cc_final: 0.8382 (t80) REVERT: E 103 LEU cc_start: 0.9498 (mm) cc_final: 0.9255 (mm) REVERT: E 117 VAL cc_start: 0.9445 (m) cc_final: 0.9242 (m) REVERT: F 44 LYS cc_start: 0.9399 (mtmt) cc_final: 0.9191 (tmtt) REVERT: F 59 LYS cc_start: 0.9764 (tptp) cc_final: 0.9466 (tptp) REVERT: F 61 PHE cc_start: 0.9250 (t80) cc_final: 0.8909 (t80) REVERT: F 63 GLU cc_start: 0.9205 (pp20) cc_final: 0.8742 (pp20) REVERT: K 55 GLN cc_start: 0.7833 (tp40) cc_final: 0.7384 (mm110) REVERT: K 108 ASN cc_start: 0.8147 (t0) cc_final: 0.7904 (m-40) REVERT: L 53 GLU cc_start: 0.9026 (tt0) cc_final: 0.8629 (tt0) REVERT: O 93 GLN cc_start: 0.9717 (tp-100) cc_final: 0.9493 (tm-30) REVERT: P 59 LYS cc_start: 0.8690 (mttp) cc_final: 0.8410 (mmmt) REVERT: P 88 TYR cc_start: 0.9629 (t80) cc_final: 0.9212 (t80) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.1238 time to fit residues: 36.4321 Evaluate side-chains 130 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 41 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 121 optimal weight: 40.0000 chunk 57 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.046870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.035126 restraints weight = 243239.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.036195 restraints weight = 144552.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.036962 restraints weight = 99543.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.037494 restraints weight = 75213.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.037877 restraints weight = 61031.025| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18408 Z= 0.187 Angle : 0.760 7.596 26628 Z= 0.452 Chirality : 0.047 0.229 3032 Planarity : 0.006 0.064 1934 Dihedral : 33.210 159.910 6222 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 24.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.22 % Allowed : 2.28 % Favored : 97.50 % 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: 0.17 (0.24), residues: 1075 helix: 0.72 (0.18), residues: 770 sheet: None (None), residues: 0 loop : -1.30 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 63 TYR 0.026 0.002 TYR M 39 PHE 0.016 0.002 PHE K 67 HIS 0.009 0.001 HIS N 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.19 (18408) covalent geometry : angle 0.76037 / 0.45 (26628) hydrogen bonds : bond 0.09508 / 6.47 ( 996) hydrogen bonds : angle 4.75809 / 3.44 ( 2577) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 0.403 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9330 (tpt) cc_final: 0.9092 (mmm) REVERT: C 61 GLU cc_start: 0.9371 (OUTLIER) cc_final: 0.8799 (tt0) REVERT: C 64 GLU cc_start: 0.9286 (tp30) cc_final: 0.8814 (tp30) REVERT: E 67 PHE cc_start: 0.8850 (t80) cc_final: 0.8439 (t80) REVERT: E 71 VAL cc_start: 0.9404 (t) cc_final: 0.9204 (t) REVERT: E 117 VAL cc_start: 0.9420 (m) cc_final: 0.9166 (m) REVERT: F 61 PHE cc_start: 0.9244 (t80) cc_final: 0.8937 (t80) REVERT: F 72 TYR cc_start: 0.9395 (m-10) cc_final: 0.8863 (m-10) REVERT: F 92 ARG cc_start: 0.9330 (mmm160) cc_final: 0.8740 (mmm160) REVERT: K 55 GLN cc_start: 0.7889 (tp40) cc_final: 0.7421 (mm110) REVERT: K 108 ASN cc_start: 0.8162 (t0) cc_final: 0.7917 (m-40) REVERT: L 53 GLU cc_start: 0.8859 (tt0) cc_final: 0.8559 (tt0) REVERT: N 62 PHE cc_start: 0.9777 (t80) cc_final: 0.9556 (t80) REVERT: O 93 GLN cc_start: 0.9788 (tp-100) cc_final: 0.9525 (tm-30) REVERT: P 59 LYS cc_start: 0.8669 (mttp) cc_final: 0.8339 (mmmt) REVERT: P 88 TYR cc_start: 0.9643 (t80) cc_final: 0.9239 (t80) REVERT: P 98 TYR cc_start: 0.8573 (m-80) cc_final: 0.8135 (m-80) outliers start: 2 outliers final: 0 residues processed: 189 average time/residue: 0.1257 time to fit residues: 35.6110 Evaluate side-chains 130 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 32 optimal weight: 0.1980 chunk 54 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 123 optimal weight: 50.0000 chunk 21 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 108 optimal weight: 40.0000 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 GLN ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.048898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.036896 restraints weight = 235398.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.038050 restraints weight = 138277.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.038857 restraints weight = 94718.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.039447 restraints weight = 71205.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.039861 restraints weight = 57108.019| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18408 Z= 0.158 Angle : 0.753 7.906 26628 Z= 0.444 Chirality : 0.047 0.316 3032 Planarity : 0.005 0.056 1934 Dihedral : 33.063 158.835 6222 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.11 % Allowed : 2.61 % Favored : 97.28 % 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: 0.18 (0.24), residues: 1075 helix: 0.72 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -1.32 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG F 67 TYR 0.025 0.002 TYR M 39 PHE 0.013 0.002 PHE K 67 HIS 0.009 0.001 HIS N 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.16 (18408) covalent geometry : angle 0.75316 / 0.44 (26628) hydrogen bonds : bond 0.06624 / 4.58 ( 996) hydrogen bonds : angle 4.44608 / 3.20 ( 2577) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.349 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: 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 70 LEU cc_start: 0.9793 (mp) cc_final: 0.9570 (pp) REVERT: A 100 LEU cc_start: 0.9829 (mt) cc_final: 0.9521 (pp) REVERT: A 120 MET cc_start: 0.9246 (tpt) cc_final: 0.9034 (mmm) REVERT: C 64 GLU cc_start: 0.9206 (tp30) cc_final: 0.8779 (tp30) REVERT: D 65 ASP cc_start: 0.9684 (t0) cc_final: 0.9285 (t0) REVERT: D 69 ARG cc_start: 0.9222 (mtp180) cc_final: 0.8631 (ptp-110) REVERT: E 67 PHE cc_start: 0.8802 (t80) cc_final: 0.8356 (t80) REVERT: E 71 VAL cc_start: 0.9414 (t) cc_final: 0.9200 (t) REVERT: E 103 LEU cc_start: 0.9516 (mm) cc_final: 0.9285 (mm) REVERT: F 59 LYS cc_start: 0.9768 (tptp) cc_final: 0.9474 (tptp) REVERT: F 61 PHE cc_start: 0.9285 (t80) cc_final: 0.8932 (t80) REVERT: F 63 GLU cc_start: 0.9366 (pp20) cc_final: 0.8789 (pp20) REVERT: K 55 GLN cc_start: 0.7851 (tp40) cc_final: 0.7396 (mm110) REVERT: N 62 PHE cc_start: 0.9774 (t80) cc_final: 0.9537 (t80) REVERT: N 70 ILE cc_start: 0.9490 (mm) cc_final: 0.9284 (tp) REVERT: O 93 GLN cc_start: 0.9751 (tp-100) cc_final: 0.9461 (tm-30) REVERT: P 59 LYS cc_start: 0.8730 (mttp) cc_final: 0.8465 (mmmt) REVERT: P 88 TYR cc_start: 0.9622 (t80) cc_final: 0.9214 (t80) REVERT: P 98 TYR cc_start: 0.8427 (m-80) cc_final: 0.7976 (m-80) outliers start: 1 outliers final: 1 residues processed: 198 average time/residue: 0.1397 time to fit residues: 40.6689 Evaluate side-chains 136 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 8.9990 chunk 125 optimal weight: 50.0000 chunk 121 optimal weight: 50.0000 chunk 85 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 52 optimal weight: 0.0670 chunk 21 optimal weight: 4.9990 chunk 110 optimal weight: 40.0000 chunk 95 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 overall best weight: 5.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** K 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.046478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.034748 restraints weight = 246348.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.035854 restraints weight = 147729.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.036594 restraints weight = 101695.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.037145 restraints weight = 77084.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.037526 restraints weight = 62346.897| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 18408 Z= 0.218 Angle : 0.785 7.470 26628 Z= 0.464 Chirality : 0.047 0.234 3032 Planarity : 0.006 0.058 1934 Dihedral : 33.082 161.459 6222 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 28.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: 0.15 (0.24), residues: 1075 helix: 0.71 (0.18), residues: 764 sheet: None (None), residues: 0 loop : -1.32 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 23 TYR 0.023 0.002 TYR M 39 PHE 0.034 0.002 PHE K 104 HIS 0.011 0.002 HIS N 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.22 (18408) covalent geometry : angle 0.78547 / 0.46 (26628) hydrogen bonds : bond 0.11504 / 7.76 ( 996) hydrogen bonds : angle 4.71802 / 3.40 ( 2577) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 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: 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: symmetry clash REVERT: B 84 MET cc_start: 0.9464 (ppp) cc_final: 0.9232 (ppp) REVERT: C 64 GLU cc_start: 0.9297 (tp30) cc_final: 0.8891 (tp30) REVERT: D 69 ARG cc_start: 0.9180 (mtp180) cc_final: 0.8926 (ttm110) REVERT: E 67 PHE cc_start: 0.8866 (t80) cc_final: 0.8425 (t80) REVERT: F 59 LYS cc_start: 0.9794 (tptp) cc_final: 0.9578 (tptp) REVERT: F 61 PHE cc_start: 0.9302 (t80) cc_final: 0.9069 (t80) REVERT: K 55 GLN cc_start: 0.7867 (tp40) cc_final: 0.7390 (mm110) REVERT: L 53 GLU cc_start: 0.8740 (tt0) cc_final: 0.8459 (tt0) REVERT: O 93 GLN cc_start: 0.9718 (tp-100) cc_final: 0.9464 (tm-30) REVERT: P 59 LYS cc_start: 0.8693 (mttp) cc_final: 0.8359 (mmmt) REVERT: P 88 TYR cc_start: 0.9648 (t80) cc_final: 0.9252 (t80) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1256 time to fit residues: 32.9747 Evaluate side-chains 125 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 80 optimal weight: 20.0000 chunk 125 optimal weight: 50.0000 chunk 56 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 131 optimal weight: 50.0000 chunk 73 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 134 optimal weight: 40.0000 chunk 48 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.047114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.035359 restraints weight = 242469.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.036449 restraints weight = 144508.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.037214 restraints weight = 99911.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.037784 restraints weight = 75493.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.038166 restraints weight = 60784.017| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18408 Z= 0.182 Angle : 0.758 7.538 26628 Z= 0.448 Chirality : 0.047 0.247 3032 Planarity : 0.005 0.065 1934 Dihedral : 33.165 161.962 6222 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 24.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: 0.21 (0.24), residues: 1075 helix: 0.75 (0.18), residues: 764 sheet: None (None), residues: 0 loop : -1.27 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 32 TYR 0.021 0.001 TYR P 72 PHE 0.039 0.002 PHE K 104 HIS 0.009 0.002 HIS N 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.18 (18408) covalent geometry : angle 0.75769 / 0.45 (26628) hydrogen bonds : bond 0.08818 / 5.99 ( 996) hydrogen bonds : angle 4.72250 / 3.39 ( 2577) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.344 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9386 (tpt) cc_final: 0.9135 (mmm) REVERT: C 64 GLU cc_start: 0.9272 (tp30) cc_final: 0.8912 (tp30) REVERT: D 69 ARG cc_start: 0.9382 (mtp180) cc_final: 0.9148 (ttm110) REVERT: E 67 PHE cc_start: 0.9025 (t80) cc_final: 0.8542 (t80) REVERT: F 59 LYS cc_start: 0.9840 (tptp) cc_final: 0.9629 (tptp) REVERT: F 61 PHE cc_start: 0.9435 (t80) cc_final: 0.9166 (t80) REVERT: F 92 ARG cc_start: 0.9401 (mmm160) cc_final: 0.8888 (mmm-85) REVERT: K 55 GLN cc_start: 0.7776 (tp40) cc_final: 0.7322 (mm110) REVERT: L 53 GLU cc_start: 0.8723 (tt0) cc_final: 0.8431 (tt0) REVERT: O 93 GLN cc_start: 0.9741 (tp-100) cc_final: 0.9464 (tm-30) REVERT: P 59 LYS cc_start: 0.8724 (mttp) cc_final: 0.8419 (mmmt) REVERT: P 88 TYR cc_start: 0.9588 (t80) cc_final: 0.9197 (t80) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1257 time to fit residues: 32.9166 Evaluate side-chains 129 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 56 optimal weight: 20.0000 chunk 10 optimal weight: 0.7980 chunk 101 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 127 optimal weight: 50.0000 chunk 142 optimal weight: 40.0000 chunk 141 optimal weight: 20.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.046618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.034939 restraints weight = 243631.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.036022 restraints weight = 145187.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.036763 restraints weight = 100623.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.037315 restraints weight = 76351.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.037619 restraints weight = 61706.644| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18408 Z= 0.193 Angle : 0.765 7.334 26628 Z= 0.452 Chirality : 0.047 0.248 3032 Planarity : 0.006 0.064 1934 Dihedral : 33.176 162.187 6222 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 26.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 0.16 (0.24), residues: 1075 helix: 0.70 (0.18), residues: 764 sheet: None (None), residues: 0 loop : -1.25 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 52 TYR 0.016 0.002 TYR P 72 PHE 0.041 0.002 PHE K 104 HIS 0.008 0.002 HIS N 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.19 (18408) covalent geometry : angle 0.76461 / 0.45 (26628) hydrogen bonds : bond 0.10061 / 6.82 ( 996) hydrogen bonds : angle 4.74079 / 3.42 ( 2577) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.446 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9392 (tpt) cc_final: 0.9143 (mmm) REVERT: C 64 GLU cc_start: 0.9310 (tp30) cc_final: 0.8954 (tp30) REVERT: D 69 ARG cc_start: 0.9355 (mtp180) cc_final: 0.9138 (ttm110) REVERT: E 67 PHE cc_start: 0.9016 (t80) cc_final: 0.8537 (t80) REVERT: F 59 LYS cc_start: 0.9838 (tptp) cc_final: 0.9624 (tptp) REVERT: F 61 PHE cc_start: 0.9427 (t80) cc_final: 0.9143 (t80) REVERT: F 92 ARG cc_start: 0.9382 (mmm160) cc_final: 0.8884 (mmm-85) REVERT: K 55 GLN cc_start: 0.7729 (tp40) cc_final: 0.7288 (mm110) REVERT: L 53 GLU cc_start: 0.8667 (tt0) cc_final: 0.8354 (tt0) REVERT: O 93 GLN cc_start: 0.9731 (tp-100) cc_final: 0.9461 (tm-30) REVERT: P 59 LYS cc_start: 0.8720 (mttp) cc_final: 0.8419 (mmmt) REVERT: P 88 TYR cc_start: 0.9606 (t80) cc_final: 0.9208 (t80) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1186 time to fit residues: 31.5455 Evaluate side-chains 120 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 36 optimal weight: 30.0000 chunk 100 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 139 optimal weight: 40.0000 chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 108 optimal weight: 40.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.047097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.035404 restraints weight = 241436.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.036512 restraints weight = 143487.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.037258 restraints weight = 98716.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.037815 restraints weight = 75003.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.038211 restraints weight = 60557.204| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18408 Z= 0.176 Angle : 0.758 8.390 26628 Z= 0.447 Chirality : 0.047 0.254 3032 Planarity : 0.005 0.077 1934 Dihedral : 33.186 162.018 6222 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 24.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: 0.17 (0.24), residues: 1075 helix: 0.71 (0.18), residues: 764 sheet: None (None), residues: 0 loop : -1.24 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 52 TYR 0.045 0.002 TYR P 98 PHE 0.041 0.002 PHE K 104 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.18 (18408) covalent geometry : angle 0.75819 / 0.45 (26628) hydrogen bonds : bond 0.08929 / 6.07 ( 996) hydrogen bonds : angle 4.68655 / 3.38 ( 2577) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2613.47 seconds wall clock time: 46 minutes 11.15 seconds (2771.15 seconds total)