Starting phenix.real_space_refine on Thu Aug 6 22:17:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w74_65716/08_2026/9w74_65716.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w74_65716/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9w74_65716/08_2026/9w74_65716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w74_65716/08_2026/9w74_65716.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w74_65716/08_2026/9w74_65716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w74_65716/08_2026/9w74_65716.map" } 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-2.2rc3-6140/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: 3.33, per 1000 atoms: 0.19 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: 1.01 Conformation dependent library (CDL) restraints added in 346.8 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: 2.52 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: 4.26 Time building geometry restraints manager: 1.40 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: 24208 1.68 - 3.35: 2271 3.35 - 5.03: 122 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: 2.570 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: 0.190 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.860 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.260 ------------------------------------------------------------------------------- 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 : 0.923 8.380 26628 Z= 0.826 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 0.92349 / 0.83 (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 : 0.301 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: A 120 MET cc_start: 0.9334 (tpt) cc_final: 0.9093 (mmm) REVERT: A 130 ILE cc_start: 0.9515 (mp) cc_final: 0.8527 (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: 0.9085 (m-30) REVERT: E 129 ARG cc_start: 0.9721 (tpp-160) cc_final: 0.9416 (tmm160) REVERT: F 44 LYS cc_start: 0.9476 (mtmt) cc_final: 0.9219 (mmmt) REVERT: F 61 PHE cc_start: 0.9156 (t80) cc_final: 0.8914 (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: 0.7986 (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: 0.1208 time to fit residues: 33.4555 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 : 0.480 ------------------------------------------------------------------------------- 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: 50.0000 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 = 0.045788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.034088 restraints weight = 249460.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.035097 restraints weight = 150367.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.035825 restraints weight = 104452.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.036367 restraints weight = 79702.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.036754 restraints weight = 64459.961| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18408 Z= 0.245 Angle : 0.837 9.398 26628 Z= 0.487 Chirality : 0.050 0.245 3032 Planarity : 0.006 0.065 1934 Dihedral : 33.176 168.868 6222 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 32.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.43 % Allowed : 7.61 % Favored : 91.96 % 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 : -1.45 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG E 131 TYR 0.021 0.002 TYR P 72 PHE 0.036 0.003 PHE K 104 HIS 0.009 0.002 HIS N 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.25 (18408) covalent geometry : angle 0.83691 / 0.49 (26628) hydrogen bonds : bond 0.12621 / 8.48 ( 996) hydrogen bonds : angle 4.98778 / 3.62 ( 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: 4 poor density : 174 time to evaluate : 0.292 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: C 64 GLU cc_start: 0.9227 (tp30) cc_final: 0.8789 (tp30) REVERT: E 67 PHE cc_start: 0.8809 (t80) cc_final: 0.8415 (t80) REVERT: F 61 PHE cc_start: 0.9107 (t80) cc_final: 0.8899 (t80) REVERT: K 55 GLN cc_start: 0.7770 (tp40) cc_final: 0.7324 (mm110) REVERT: K 108 ASN cc_start: 0.8233 (t0) cc_final: 0.7995 (m-40) REVERT: L 53 GLU cc_start: 0.9087 (tt0) cc_final: 0.8795 (tt0) REVERT: M 95 LYS cc_start: 0.9460 (tppt) cc_final: 0.9250 (tmmt) REVERT: O 93 GLN cc_start: 0.9753 (tp-100) cc_final: 0.9267 (tm-30) REVERT: P 59 LYS cc_start: 0.8809 (mttp) cc_final: 0.8444 (mmmt) REVERT: P 88 TYR cc_start: 0.9654 (t80) cc_final: 0.9246 (t80) outliers start: 4 outliers final: 2 residues processed: 178 average time/residue: 0.1140 time to fit residues: 31.0398 Evaluate side-chains 122 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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: 7.9990 chunk 125 optimal weight: 50.0000 chunk 112 optimal weight: 40.0000 chunk 43 optimal weight: 5.9990 chunk 63 optimal weight: 50.0000 chunk 3 optimal weight: 4.9990 chunk 127 optimal weight: 50.0000 chunk 12 optimal weight: 0.9980 chunk 87 optimal weight: 30.0000 chunk 113 optimal weight: 30.0000 overall best weight: 4.1386 ------------------------------------------------------------------------------- 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** ** E 108 ASN ** 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 = 0.3199 r_free = 0.3199 target = 0.046784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.034851 restraints weight = 245992.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.035947 restraints weight = 148102.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.036713 restraints weight = 101420.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.037276 restraints weight = 76445.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.037661 restraints weight = 61567.553| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18408 Z= 0.188 Angle : 0.776 7.903 26628 Z= 0.459 Chirality : 0.048 0.252 3032 Planarity : 0.005 0.062 1934 Dihedral : 33.170 164.954 6222 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 26.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.33 % Allowed : 4.89 % Favored : 94.78 % 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: 0.73 (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 0.010 0.001 ARG E 131 TYR 0.031 0.002 TYR M 39 PHE 0.033 0.002 PHE K 104 HIS 0.006 0.002 HIS N 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.19 (18408) covalent geometry : angle 0.77597 / 0.46 (26628) hydrogen bonds : bond 0.09722 / 6.59 ( 996) hydrogen bonds : angle 4.78900 / 3.47 ( 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 188 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 185 time to evaluate : 0.294 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: C 64 GLU cc_start: 0.9193 (tp30) cc_final: 0.8721 (tp30) REVERT: D 69 ARG cc_start: 0.9188 (mtp180) cc_final: 0.8902 (ptm160) REVERT: E 67 PHE cc_start: 0.8863 (t80) cc_final: 0.8418 (t80) REVERT: F 61 PHE cc_start: 0.9148 (t80) cc_final: 0.8937 (t80) REVERT: K 55 GLN cc_start: 0.7770 (tp40) cc_final: 0.7339 (mm110) REVERT: K 108 ASN cc_start: 0.8144 (t0) cc_final: 0.7876 (m-40) REVERT: L 53 GLU cc_start: 0.9050 (tt0) cc_final: 0.8743 (tt0) REVERT: M 95 LYS cc_start: 0.9461 (tppt) cc_final: 0.9255 (tmmt) REVERT: M 104 GLN cc_start: 0.6788 (OUTLIER) cc_final: 0.6303 (pp30) REVERT: O 93 GLN cc_start: 0.9740 (tp-100) cc_final: 0.9244 (tm-30) REVERT: P 59 LYS cc_start: 0.8661 (mttp) cc_final: 0.8329 (mmmt) REVERT: P 88 TYR cc_start: 0.9640 (t80) cc_final: 0.9225 (t80) REVERT: P 98 TYR cc_start: 0.8571 (m-80) cc_final: 0.8127 (m-80) outliers start: 3 outliers final: 0 residues processed: 188 average time/residue: 0.1343 time to fit residues: 37.2877 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 : 0.451 ------------------------------------------------------------------------------- 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: 1.9990 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 137 optimal weight: 30.0000 chunk 122 optimal weight: 50.0000 chunk 21 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 107 optimal weight: 40.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** ** E 108 ASN ** 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 = 0.3191 r_free = 0.3191 target = 0.046512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.034683 restraints weight = 245494.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.035739 restraints weight = 146242.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.036486 restraints weight = 101296.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.037023 restraints weight = 76572.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.037415 restraints weight = 62164.510| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18408 Z= 0.197 Angle : 0.778 7.531 26628 Z= 0.459 Chirality : 0.048 0.251 3032 Planarity : 0.005 0.055 1934 Dihedral : 33.165 163.070 6222 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 26.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: 0.22 (0.24), residues: 1075 helix: 0.79 (0.18), residues: 770 sheet: None (None), residues: 0 loop : -1.39 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 92 TYR 0.030 0.002 TYR M 39 PHE 0.017 0.002 PHE K 67 HIS 0.006 0.002 HIS N 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.20 (18408) covalent geometry : angle 0.77782 / 0.46 (26628) hydrogen bonds : bond 0.10403 / 7.05 ( 996) hydrogen bonds : angle 4.76423 / 3.45 ( 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 179 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.9243 (tp30) cc_final: 0.8748 (tp30) REVERT: D 68 GLU cc_start: 0.9411 (mt-10) cc_final: 0.9204 (mt-10) REVERT: E 67 PHE cc_start: 0.8862 (t80) cc_final: 0.8431 (t80) REVERT: F 59 LYS cc_start: 0.9781 (tptp) cc_final: 0.9570 (tptp) REVERT: F 61 PHE cc_start: 0.9103 (t80) cc_final: 0.8893 (t80) REVERT: K 55 GLN cc_start: 0.7763 (tp40) cc_final: 0.7331 (mm110) REVERT: K 108 ASN cc_start: 0.8196 (t0) cc_final: 0.7988 (m-40) REVERT: L 53 GLU cc_start: 0.9065 (tt0) cc_final: 0.8757 (tt0) REVERT: O 93 GLN cc_start: 0.9735 (tp-100) cc_final: 0.9249 (tm-30) REVERT: P 59 LYS cc_start: 0.8672 (mttp) cc_final: 0.8330 (mmmt) REVERT: P 88 TYR cc_start: 0.9658 (t80) cc_final: 0.9249 (t80) REVERT: P 98 TYR cc_start: 0.8486 (m-80) cc_final: 0.8163 (m-80) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1283 time to fit residues: 34.8841 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 : 0.472 ------------------------------------------------------------------------------- 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: 6.9990 chunk 85 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 115 optimal weight: 50.0000 chunk 38 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- 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** ** 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 = 0.3189 r_free = 0.3189 target = 0.046369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.034654 restraints weight = 244097.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.035692 restraints weight = 145386.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.036433 restraints weight = 100883.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.036891 restraints weight = 76408.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.037323 restraints weight = 62832.179| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18408 Z= 0.200 Angle : 0.780 7.331 26628 Z= 0.460 Chirality : 0.048 0.251 3032 Planarity : 0.006 0.056 1934 Dihedral : 33.188 162.369 6222 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 27.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.11 % Allowed : 3.80 % Favored : 96.09 % 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: 0.75 (0.18), residues: 770 sheet: None (None), residues: 0 loop : -1.41 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 67 TYR 0.028 0.002 TYR M 39 PHE 0.027 0.002 PHE E 104 HIS 0.007 0.002 HIS N 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.20 (18408) covalent geometry : angle 0.77968 / 0.46 (26628) hydrogen bonds : bond 0.10473 / 7.10 ( 996) hydrogen bonds : angle 4.81804 / 3.49 ( 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 180 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.361 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: 0.9315 (tpt) cc_final: 0.9073 (mmm) REVERT: A 130 ILE cc_start: 0.9671 (mp) cc_final: 0.9247 (tp) REVERT: B 84 MET cc_start: 0.9469 (ppp) cc_final: 0.9208 (ppp) REVERT: C 64 GLU cc_start: 0.9240 (tp30) cc_final: 0.8739 (tp30) REVERT: E 67 PHE cc_start: 0.8850 (t80) cc_final: 0.8444 (t80) REVERT: E 71 VAL cc_start: 0.9407 (t) cc_final: 0.9206 (t) REVERT: E 90 MET cc_start: 0.9561 (mmp) cc_final: 0.9327 (mmm) REVERT: F 59 LYS cc_start: 0.9786 (tptp) cc_final: 0.9570 (tptp) REVERT: F 61 PHE cc_start: 0.9209 (t80) cc_final: 0.8998 (t80) REVERT: K 55 GLN cc_start: 0.7893 (tp40) cc_final: 0.7428 (mm110) REVERT: K 108 ASN cc_start: 0.8236 (t0) cc_final: 0.8003 (m-40) REVERT: N 62 PHE cc_start: 0.9779 (t80) cc_final: 0.9553 (t80) REVERT: O 93 GLN cc_start: 0.9739 (tp-100) cc_final: 0.9255 (tm-30) REVERT: P 59 LYS cc_start: 0.8667 (mttp) cc_final: 0.8351 (mmmt) REVERT: P 88 TYR cc_start: 0.9648 (t80) cc_final: 0.9241 (t80) REVERT: P 98 TYR cc_start: 0.8561 (m-80) cc_final: 0.8071 (m-80) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.1151 time to fit residues: 31.9788 Evaluate side-chains 124 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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: 0.9980 chunk 14 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 11 optimal weight: 30.0000 chunk 92 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 121 optimal weight: 40.0000 chunk 57 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.046889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.035157 restraints weight = 252701.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.036218 restraints weight = 149362.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.036965 restraints weight = 102943.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.037512 restraints weight = 78269.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.037798 restraints weight = 63505.988| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1572 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= 0.182 Angle : 0.768 8.090 26628 Z= 0.452 Chirality : 0.047 0.252 3032 Planarity : 0.005 0.057 1934 Dihedral : 33.177 161.374 6222 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 24.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.22 % Allowed : 2.83 % Favored : 96.96 % 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: 0.72 (0.18), residues: 770 sheet: None (None), residues: 0 loop : -1.36 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 131 TYR 0.028 0.002 TYR M 39 PHE 0.017 0.002 PHE E 104 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.18 (18408) covalent geometry : angle 0.76761 / 0.45 (26628) hydrogen bonds : bond 0.09323 / 6.35 ( 996) hydrogen bonds : angle 4.72344 / 3.42 ( 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 184 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 0.370 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 130 ILE cc_start: 0.9704 (mp) cc_final: 0.9253 (tp) REVERT: C 64 GLU cc_start: 0.9268 (tp30) cc_final: 0.8854 (tp30) REVERT: E 67 PHE cc_start: 0.9012 (t80) cc_final: 0.8549 (t80) REVERT: F 59 LYS cc_start: 0.9837 (tptp) cc_final: 0.9632 (tptp) REVERT: F 72 TYR cc_start: 0.9427 (m-10) cc_final: 0.8900 (m-10) REVERT: F 92 ARG cc_start: 0.9383 (mmm160) cc_final: 0.8771 (mmm160) REVERT: K 55 GLN cc_start: 0.7704 (tp40) cc_final: 0.7285 (mm110) REVERT: K 108 ASN cc_start: 0.8218 (t0) cc_final: 0.7976 (m-40) REVERT: K 124 ILE cc_start: 0.9024 (mt) cc_final: 0.8818 (mp) REVERT: O 93 GLN cc_start: 0.9754 (tp-100) cc_final: 0.9502 (tm-30) REVERT: P 59 LYS cc_start: 0.8688 (mttp) cc_final: 0.8399 (mmmt) REVERT: P 88 TYR cc_start: 0.9609 (t80) cc_final: 0.9226 (t80) outliers start: 2 outliers final: 0 residues processed: 184 average time/residue: 0.1315 time to fit residues: 36.9344 Evaluate side-chains 133 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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: 7.9990 chunk 54 optimal weight: 5.9990 chunk 90 optimal weight: 30.0000 chunk 41 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 123 optimal weight: 50.0000 chunk 21 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 108 optimal weight: 40.0000 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 GLN ** 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 = 0.3235 r_free = 0.3235 target = 0.048108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.036176 restraints weight = 237767.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.037301 restraints weight = 141261.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.038094 restraints weight = 96065.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.038658 restraints weight = 72149.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.039053 restraints weight = 58302.552| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18408 Z= 0.159 Angle : 0.757 8.217 26628 Z= 0.445 Chirality : 0.047 0.268 3032 Planarity : 0.005 0.055 1934 Dihedral : 33.030 160.334 6222 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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: 0.27 (0.24), residues: 1075 helix: 0.80 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -1.31 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 52 TYR 0.026 0.002 TYR M 39 PHE 0.022 0.002 PHE K 104 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.16 (18408) covalent geometry : angle 0.75662 / 0.44 (26628) hydrogen bonds : bond 0.07320 / 5.03 ( 996) hydrogen bonds : angle 4.51322 / 3.25 ( 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 194 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9279 (tpt) cc_final: 0.9026 (mmm) REVERT: A 130 ILE cc_start: 0.9619 (mp) cc_final: 0.9330 (tp) REVERT: C 61 GLU cc_start: 0.7457 (tp30) cc_final: 0.7097 (tm-30) REVERT: C 64 GLU cc_start: 0.9158 (tp30) cc_final: 0.8686 (tp30) REVERT: D 65 ASP cc_start: 0.9714 (t0) cc_final: 0.9364 (t0) REVERT: D 69 ARG cc_start: 0.9241 (mtp180) cc_final: 0.8691 (ptp-110) REVERT: E 67 PHE cc_start: 0.8885 (t80) cc_final: 0.8427 (t80) REVERT: E 71 VAL cc_start: 0.9435 (t) cc_final: 0.9228 (t) REVERT: E 103 LEU cc_start: 0.9438 (mm) cc_final: 0.9217 (mm) REVERT: F 59 LYS cc_start: 0.9785 (tptp) cc_final: 0.9518 (tptp) REVERT: F 63 GLU cc_start: 0.9224 (pp20) cc_final: 0.8736 (pp20) REVERT: K 55 GLN cc_start: 0.7835 (tp40) cc_final: 0.7382 (mm110) REVERT: K 108 ASN cc_start: 0.8120 (t0) cc_final: 0.7875 (m-40) REVERT: K 124 ILE cc_start: 0.9127 (mt) cc_final: 0.8911 (mp) REVERT: N 62 PHE cc_start: 0.9774 (t80) cc_final: 0.9526 (t80) REVERT: N 70 ILE cc_start: 0.9513 (mm) cc_final: 0.9313 (tp) REVERT: O 93 GLN cc_start: 0.9772 (tp-100) cc_final: 0.9538 (tm-30) REVERT: P 59 LYS cc_start: 0.8695 (mttp) cc_final: 0.8411 (mmmt) REVERT: P 88 TYR cc_start: 0.9617 (t80) cc_final: 0.9212 (t80) REVERT: P 98 TYR cc_start: 0.8443 (m-80) cc_final: 0.8002 (m-80) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1310 time to fit residues: 38.0776 Evaluate side-chains 142 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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: 6.9990 chunk 125 optimal weight: 50.0000 chunk 121 optimal weight: 40.0000 chunk 85 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 110 optimal weight: 40.0000 chunk 95 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 64 ASN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.045928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.034326 restraints weight = 248435.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.035349 restraints weight = 147657.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.036094 restraints weight = 102176.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.036629 restraints weight = 77093.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.037023 restraints weight = 62223.318| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18408 Z= 0.231 Angle : 0.803 8.135 26628 Z= 0.469 Chirality : 0.048 0.269 3032 Planarity : 0.006 0.053 1934 Dihedral : 33.080 162.738 6222 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 30.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: 0.02 (0.24), residues: 1075 helix: 0.62 (0.18), residues: 764 sheet: None (None), residues: 0 loop : -1.38 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 71 TYR 0.026 0.002 TYR M 39 PHE 0.015 0.002 PHE K 67 HIS 0.006 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.23 (18408) covalent geometry : angle 0.80341 / 0.47 (26628) hydrogen bonds : bond 0.12167 / 8.19 ( 996) hydrogen bonds : angle 4.87595 / 3.54 ( 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 182 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9491 (ppp) cc_final: 0.9276 (ppp) REVERT: C 64 GLU cc_start: 0.9264 (tp30) cc_final: 0.8833 (tp30) REVERT: E 67 PHE cc_start: 0.9050 (t80) cc_final: 0.8596 (t80) REVERT: E 99 TYR cc_start: 0.8906 (t80) cc_final: 0.8055 (t80) REVERT: E 103 LEU cc_start: 0.9544 (mm) cc_final: 0.9343 (mm) REVERT: F 59 LYS cc_start: 0.9853 (tptp) cc_final: 0.9648 (tptp) REVERT: K 55 GLN cc_start: 0.7740 (tp40) cc_final: 0.7292 (mm110) REVERT: K 108 ASN cc_start: 0.8174 (t0) cc_final: 0.7927 (m-40) REVERT: O 90 MET cc_start: 0.9704 (tpp) cc_final: 0.9480 (tpt) REVERT: O 93 GLN cc_start: 0.9785 (tp-100) cc_final: 0.9482 (tm-30) REVERT: P 59 LYS cc_start: 0.8699 (mttp) cc_final: 0.8384 (mmmt) REVERT: P 88 TYR cc_start: 0.9618 (t80) cc_final: 0.9248 (t80) REVERT: P 98 TYR cc_start: 0.8151 (m-80) cc_final: 0.7926 (m-80) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1219 time to fit residues: 33.8289 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 : 0.461 ------------------------------------------------------------------------------- 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: 6.9990 chunk 125 optimal weight: 50.0000 chunk 56 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 131 optimal weight: 50.0000 chunk 73 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 134 optimal weight: 40.0000 chunk 48 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 85 GLN ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.046245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.034539 restraints weight = 246533.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.035615 restraints weight = 147053.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.036357 restraints weight = 100838.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.036888 restraints weight = 76327.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.037287 restraints weight = 61750.765| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18408 Z= 0.200 Angle : 0.786 8.236 26628 Z= 0.460 Chirality : 0.047 0.270 3032 Planarity : 0.005 0.053 1934 Dihedral : 33.201 162.924 6222 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 27.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % 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: -0.05 (0.24), residues: 1075 helix: 0.55 (0.18), residues: 764 sheet: None (None), residues: 0 loop : -1.34 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 52 TYR 0.029 0.002 TYR M 39 PHE 0.016 0.002 PHE K 78 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.20 (18408) covalent geometry : angle 0.78641 / 0.46 (26628) hydrogen bonds : bond 0.10066 / 6.82 ( 996) hydrogen bonds : angle 4.90907 / 3.56 ( 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 176 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.314 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 120 MET cc_start: 0.9320 (tpt) cc_final: 0.9086 (mmm) REVERT: C 64 GLU cc_start: 0.9191 (tp30) cc_final: 0.8743 (tp30) REVERT: E 67 PHE cc_start: 0.8894 (t80) cc_final: 0.8483 (t80) REVERT: E 103 LEU cc_start: 0.9461 (mm) cc_final: 0.9214 (mm) REVERT: F 59 LYS cc_start: 0.9803 (tptp) cc_final: 0.9584 (tptp) REVERT: F 61 PHE cc_start: 0.9289 (t80) cc_final: 0.8957 (t80) REVERT: K 55 GLN cc_start: 0.7829 (tp40) cc_final: 0.7352 (mm110) REVERT: K 108 ASN cc_start: 0.8210 (t0) cc_final: 0.7987 (m-40) REVERT: O 93 GLN cc_start: 0.9773 (tp-100) cc_final: 0.9416 (tm-30) REVERT: P 59 LYS cc_start: 0.8666 (mttp) cc_final: 0.8360 (mmmt) REVERT: P 88 TYR cc_start: 0.9615 (t80) cc_final: 0.9217 (t80) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1223 time to fit residues: 32.9922 Evaluate side-chains 124 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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: 2.9990 chunk 10 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 22 optimal weight: 0.0670 chunk 70 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 127 optimal weight: 50.0000 chunk 142 optimal weight: 40.0000 chunk 141 optimal weight: 30.0000 overall best weight: 2.6124 ------------------------------------------------------------------------------- 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 ASN ** 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 = 0.3227 r_free = 0.3227 target = 0.047666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.035876 restraints weight = 238923.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.036962 restraints weight = 141121.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.037707 restraints weight = 97422.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.038289 restraints weight = 73707.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.038695 restraints weight = 59325.562| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18408 Z= 0.164 Angle : 0.765 7.486 26628 Z= 0.449 Chirality : 0.047 0.281 3032 Planarity : 0.005 0.052 1934 Dihedral : 33.088 161.215 6222 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 21.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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: 0.15 (0.25), residues: 1075 helix: 0.71 (0.18), residues: 766 sheet: None (None), residues: 0 loop : -1.32 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 52 TYR 0.023 0.002 TYR M 39 PHE 0.021 0.002 PHE O 104 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.16 (18408) covalent geometry : angle 0.76547 / 0.45 (26628) hydrogen bonds : bond 0.07686 / 5.27 ( 996) hydrogen bonds : angle 4.71259 / 3.41 ( 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 181 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9288 (tpt) cc_final: 0.9033 (mmm) REVERT: C 64 GLU cc_start: 0.9156 (tp30) cc_final: 0.8696 (tp30) REVERT: E 67 PHE cc_start: 0.8899 (t80) cc_final: 0.8461 (t80) REVERT: E 71 VAL cc_start: 0.9427 (t) cc_final: 0.9223 (t) REVERT: F 59 LYS cc_start: 0.9792 (tptp) cc_final: 0.9510 (tptp) REVERT: F 61 PHE cc_start: 0.9277 (t80) cc_final: 0.8978 (t80) REVERT: F 63 GLU cc_start: 0.9201 (pp20) cc_final: 0.8681 (pp20) REVERT: F 92 ARG cc_start: 0.9333 (mmm160) cc_final: 0.8867 (mmm-85) REVERT: K 55 GLN cc_start: 0.7837 (tp40) cc_final: 0.7389 (mm110) REVERT: K 108 ASN cc_start: 0.8139 (t0) cc_final: 0.7910 (m-40) REVERT: O 93 GLN cc_start: 0.9764 (tp-100) cc_final: 0.9524 (tm-30) REVERT: P 59 LYS cc_start: 0.8691 (mttp) cc_final: 0.8392 (mmmt) REVERT: P 88 TYR cc_start: 0.9594 (t80) cc_final: 0.9188 (t80) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1314 time to fit residues: 35.7920 Evaluate side-chains 133 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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: 0.9980 chunk 101 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 139 optimal weight: 40.0000 chunk 6 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 108 optimal weight: 40.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 ASN ** 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 = 0.3196 r_free = 0.3196 target = 0.046454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.034860 restraints weight = 244952.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.035918 restraints weight = 146566.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.036667 restraints weight = 100902.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.037198 restraints weight = 76479.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.037585 restraints weight = 61846.205| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18408 Z= 0.203 Angle : 0.784 9.277 26628 Z= 0.460 Chirality : 0.047 0.274 3032 Planarity : 0.005 0.053 1934 Dihedral : 33.079 162.497 6222 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 27.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % 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: 0.04 (0.24), residues: 1075 helix: 0.62 (0.18), residues: 758 sheet: None (None), residues: 0 loop : -1.28 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 52 TYR 0.035 0.002 TYR E 99 PHE 0.014 0.002 PHE O 104 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.20 (18408) covalent geometry : angle 0.78441 / 0.46 (26628) hydrogen bonds : bond 0.10326 / 6.99 ( 996) hydrogen bonds : angle 4.84990 / 3.52 ( 2577) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2584.05 seconds wall clock time: 45 minutes 35.02 seconds (2735.02 seconds total)