Starting phenix.real_space_refine on Mon Jan 20 03:09:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vfz_43195/01_2025/8vfz_43195.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vfz_43195/01_2025/8vfz_43195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vfz_43195/01_2025/8vfz_43195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vfz_43195/01_2025/8vfz_43195.map" model { file = "/net/cci-nas-00/data/ceres_data/8vfz_43195/01_2025/8vfz_43195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vfz_43195/01_2025/8vfz_43195.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.001 sd= 0.030 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 342 5.49 5 S 28 5.16 5 C 8336 2.51 5 N 2764 2.21 5 O 3436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 14906 Number of models: 1 Model: "" Number of chains: 12 Chain: "O" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 856 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain: "I" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3501 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "J" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3510 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "P" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 856 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain: "G" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 931 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Time building chain proxies: 8.79, per 1000 atoms: 0.59 Number of scatterers: 14906 At special positions: 0 Unit cell: (81.84, 137.28, 199.32, 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 28 16.00 P 342 15.00 O 3436 8.00 N 2764 7.00 C 8336 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: 3.39 Conformation dependent library (CDL) restraints added in 1.2 seconds 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 66.8% alpha, 2.8% beta 171 base pairs and 289 stacking pairs defined. Time for finding SS restraints: 6.85 Creating SS restraints... Processing helix chain 'O' and resid 174 through 186 Processing helix chain 'O' and resid 192 through 204 Processing helix chain 'O' and resid 205 through 209 removed outlier: 3.522A pdb=" N GLN O 209 " --> pdb=" O TYR O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 225 removed outlier: 3.744A pdb=" N TRP O 214 " --> pdb=" O ASN O 210 " (cutoff:3.500A) Processing helix chain 'O' and resid 248 through 251 removed outlier: 3.625A pdb=" N GLY O 251 " --> pdb=" O PRO O 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 248 through 251' Processing helix chain 'P' and resid 174 through 186 Processing helix chain 'P' and resid 192 through 204 Processing helix chain 'P' and resid 205 through 209 removed outlier: 3.826A pdb=" N GLN P 209 " --> pdb=" O TYR P 206 " (cutoff:3.500A) Processing helix chain 'P' and resid 210 through 225 removed outlier: 3.822A pdb=" N ASN P 216 " --> pdb=" O GLN P 212 " (cutoff:3.500A) Processing helix chain 'P' and resid 248 through 251 removed outlier: 3.848A pdb=" N GLY P 251 " --> pdb=" O PRO P 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 248 through 251' Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.135A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.515A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.517A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.112A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 85 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.799A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.579A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 85 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.638A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 228 through 231 Processing sheet with id=AA2, first strand: chain 'P' and resid 228 through 231 Processing sheet with id=AA3, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.428A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.892A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.373A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.175A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 478 hydrogen bonds defined for protein. 1401 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 417 hydrogen bonds 834 hydrogen bond angles 0 basepair planarities 171 basepair parallelities 289 stacking parallelities Total time for adding SS restraints: 6.45 Time building geometry restraints manager: 3.96 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: 2587 1.33 - 1.45: 5293 1.45 - 1.57: 7287 1.57 - 1.69: 682 1.69 - 1.81: 46 Bond restraints: 15895 Sorted by residual: bond pdb=" N GLY G 8 " pdb=" CA GLY G 8 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.92e+00 bond pdb=" CA LYS O 264 " pdb=" C LYS O 264 " ideal model delta sigma weight residual 1.532 1.512 0.020 9.60e-03 1.09e+04 4.34e+00 bond pdb=" C SER P 234 " pdb=" N PRO P 235 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.50e+00 bond pdb=" C3' DG J 127 " pdb=" O3' DG J 127 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.39e+00 bond pdb=" C1' DC J 56 " pdb=" N1 DC J 56 " ideal model delta sigma weight residual 1.490 1.544 -0.054 3.00e-02 1.11e+03 3.19e+00 ... (remaining 15890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 21713 1.41 - 2.81: 1051 2.81 - 4.22: 143 4.22 - 5.62: 19 5.62 - 7.03: 2 Bond angle restraints: 22928 Sorted by residual: angle pdb=" C2' DT I 161 " pdb=" C1' DT I 161 " pdb=" N1 DT I 161 " ideal model delta sigma weight residual 113.50 118.33 -4.83 1.50e+00 4.44e-01 1.04e+01 angle pdb=" C3' DG J 127 " pdb=" O3' DG J 127 " pdb=" P DG J 128 " ideal model delta sigma weight residual 120.20 124.88 -4.68 1.50e+00 4.44e-01 9.72e+00 angle pdb=" C LYS O 264 " pdb=" CA LYS O 264 " pdb=" CB LYS O 264 " ideal model delta sigma weight residual 112.27 107.04 5.23 1.75e+00 3.27e-01 8.94e+00 angle pdb=" C2' DT J 54 " pdb=" C1' DT J 54 " pdb=" N1 DT J 54 " ideal model delta sigma weight residual 113.50 117.98 -4.48 1.50e+00 4.44e-01 8.94e+00 angle pdb=" C2' DC I 110 " pdb=" C1' DC I 110 " pdb=" N1 DC I 110 " ideal model delta sigma weight residual 113.50 117.85 -4.35 1.50e+00 4.44e-01 8.40e+00 ... (remaining 22923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.42: 7098 32.42 - 64.85: 1609 64.85 - 97.27: 46 97.27 - 129.69: 0 129.69 - 162.12: 2 Dihedral angle restraints: 8755 sinusoidal: 5893 harmonic: 2862 Sorted by residual: dihedral pdb=" CA LYS O 237 " pdb=" C LYS O 237 " pdb=" N PRO O 238 " pdb=" CA PRO O 238 " ideal model delta harmonic sigma weight residual 180.00 158.36 21.64 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" C4' DG J 127 " pdb=" C3' DG J 127 " pdb=" O3' DG J 127 " pdb=" P DG J 128 " ideal model delta sinusoidal sigma weight residual 220.00 57.88 162.12 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" C4' DC J 93 " pdb=" C3' DC J 93 " pdb=" O3' DC J 93 " pdb=" P DC J 94 " ideal model delta sinusoidal sigma weight residual 220.00 73.49 146.51 1 3.50e+01 8.16e-04 1.44e+01 ... (remaining 8752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1669 0.029 - 0.058: 546 0.058 - 0.087: 281 0.087 - 0.116: 55 0.116 - 0.144: 12 Chirality restraints: 2563 Sorted by residual: chirality pdb=" P DG J 128 " pdb=" OP1 DG J 128 " pdb=" OP2 DG J 128 " pdb=" O5' DG J 128 " both_signs ideal model delta sigma weight residual True 2.35 -2.49 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ILE D 89 " pdb=" N ILE D 89 " pdb=" C ILE D 89 " pdb=" CB ILE D 89 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 2560 not shown) Planarity restraints: 1719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS P 237 " -0.062 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO P 238 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO P 238 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO P 238 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS O 237 " -0.051 5.00e-02 4.00e+02 7.70e-02 9.48e+00 pdb=" N PRO O 238 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO O 238 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO O 238 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 140 " 0.032 2.00e-02 2.50e+03 1.60e-02 6.41e+00 pdb=" N1 DT I 140 " -0.036 2.00e-02 2.50e+03 pdb=" C2 DT I 140 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DT I 140 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT I 140 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT I 140 " 0.007 2.00e-02 2.50e+03 pdb=" O4 DT I 140 " 0.012 2.00e-02 2.50e+03 pdb=" C5 DT I 140 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 140 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DT I 140 " 0.001 2.00e-02 2.50e+03 ... (remaining 1716 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 183 2.63 - 3.20: 12511 3.20 - 3.77: 28290 3.77 - 4.33: 36387 4.33 - 4.90: 52114 Nonbonded interactions: 129485 Sorted by model distance: nonbonded pdb=" OP1 DA I 144 " pdb=" OG SER H 32 " model vdw 2.063 3.040 nonbonded pdb=" O THR G 76 " pdb=" OG1 THR H 52 " model vdw 2.073 3.040 nonbonded pdb=" OP1 DG J 143 " pdb=" OG1 THR A 45 " model vdw 2.189 3.040 nonbonded pdb=" O THR C 76 " pdb=" OG1 THR D 52 " model vdw 2.218 3.040 nonbonded pdb=" OE1 GLN F 27 " pdb=" NH1 ARG F 55 " model vdw 2.235 3.120 ... (remaining 129480 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' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 10 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'O' selection = chain 'P' } 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 38.400 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 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 : 0.005 0.055 15895 Z= 0.245 Angle : 0.676 7.031 22928 Z= 0.423 Chirality : 0.037 0.144 2563 Planarity : 0.005 0.094 1719 Dihedral : 25.927 162.118 6911 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.97 % Favored : 97.72 % Rotamer: Outliers : 1.20 % Allowed : 1.92 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.28), residues: 964 helix: 3.30 (0.21), residues: 622 sheet: -1.64 (0.94), residues: 24 loop : -0.35 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 214 HIS 0.002 0.001 HIS B 75 PHE 0.008 0.001 PHE P 224 TYR 0.007 0.001 TYR B 72 ARG 0.004 0.000 ARG O 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 450 time to evaluate : 1.135 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 204 PHE cc_start: 0.9280 (m-80) cc_final: 0.9021 (m-80) REVERT: O 260 LEU cc_start: 0.4439 (OUTLIER) cc_final: 0.3684 (tt) REVERT: P 175 TYR cc_start: 0.4490 (m-80) cc_final: 0.3490 (m-10) REVERT: G 23 LEU cc_start: 0.9433 (mt) cc_final: 0.9050 (mp) REVERT: G 24 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8075 (mm-40) REVERT: G 34 LEU cc_start: 0.9645 (mt) cc_final: 0.9432 (mt) REVERT: G 50 TYR cc_start: 0.8592 (t80) cc_final: 0.8381 (t80) REVERT: G 83 LEU cc_start: 0.9576 (mt) cc_final: 0.9330 (mt) REVERT: G 87 ILE cc_start: 0.9571 (mt) cc_final: 0.9297 (tp) REVERT: G 88 ARG cc_start: 0.8798 (mmt180) cc_final: 0.8191 (mtp180) REVERT: G 100 VAL cc_start: 0.9270 (t) cc_final: 0.8998 (p) REVERT: A 50 GLU cc_start: 0.9388 (mt-10) cc_final: 0.8780 (mt-10) REVERT: A 51 ILE cc_start: 0.8280 (mt) cc_final: 0.7983 (mt) REVERT: A 54 TYR cc_start: 0.9282 (m-80) cc_final: 0.8637 (m-80) REVERT: A 92 LEU cc_start: 0.8900 (mt) cc_final: 0.8688 (mt) REVERT: A 101 VAL cc_start: 0.9237 (t) cc_final: 0.8984 (t) REVERT: A 105 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8503 (tm-30) REVERT: B 39 ARG cc_start: 0.9188 (mmt-90) cc_final: 0.8428 (tpp-160) REVERT: B 68 ASP cc_start: 0.8814 (m-30) cc_final: 0.8492 (m-30) REVERT: B 70 VAL cc_start: 0.9680 (t) cc_final: 0.9344 (m) REVERT: B 87 VAL cc_start: 0.9811 (t) cc_final: 0.9589 (t) REVERT: B 91 LYS cc_start: 0.9690 (ttpt) cc_final: 0.9213 (ptmm) REVERT: C 38 ASN cc_start: 0.8671 (m110) cc_final: 0.8297 (t0) REVERT: C 50 TYR cc_start: 0.8243 (t80) cc_final: 0.7998 (t80) REVERT: C 51 LEU cc_start: 0.9684 (tp) cc_final: 0.9477 (tp) REVERT: C 90 ASP cc_start: 0.8882 (t0) cc_final: 0.8573 (t0) REVERT: C 92 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8750 (mt-10) REVERT: D 62 MET cc_start: 0.9190 (mmm) cc_final: 0.8915 (mmm) REVERT: D 85 LYS cc_start: 0.9370 (mtpt) cc_final: 0.9059 (mmmt) REVERT: D 87 SER cc_start: 0.9418 (m) cc_final: 0.8534 (p) REVERT: D 89 ILE cc_start: 0.9390 (mt) cc_final: 0.9185 (tp) REVERT: E 48 LEU cc_start: 0.9319 (mt) cc_final: 0.8954 (mt) REVERT: E 60 LEU cc_start: 0.9209 (mt) cc_final: 0.8000 (mp) REVERT: E 73 GLU cc_start: 0.8970 (tt0) cc_final: 0.8589 (mt-10) REVERT: E 93 GLN cc_start: 0.9059 (tt0) cc_final: 0.8246 (tm-30) REVERT: E 106 ASP cc_start: 0.9057 (m-30) cc_final: 0.8590 (m-30) REVERT: E 109 LEU cc_start: 0.9646 (mt) cc_final: 0.9210 (mm) REVERT: E 125 GLN cc_start: 0.9266 (mt0) cc_final: 0.8876 (mp10) REVERT: F 58 LEU cc_start: 0.9659 (tp) cc_final: 0.9415 (tp) REVERT: F 68 ASP cc_start: 0.8909 (m-30) cc_final: 0.8691 (m-30) REVERT: F 85 ASP cc_start: 0.9098 (m-30) cc_final: 0.8795 (t0) REVERT: F 87 VAL cc_start: 0.9752 (t) cc_final: 0.9449 (t) REVERT: F 91 LYS cc_start: 0.9430 (ttpt) cc_final: 0.9149 (ptpt) REVERT: H 38 SER cc_start: 0.9131 (m) cc_final: 0.8652 (p) REVERT: H 68 ASP cc_start: 0.8760 (t0) cc_final: 0.8478 (t0) REVERT: H 90 THR cc_start: 0.8750 (p) cc_final: 0.8214 (p) REVERT: H 91 SER cc_start: 0.9118 (p) cc_final: 0.8914 (t) REVERT: H 93 GLU cc_start: 0.8666 (mp0) cc_final: 0.8332 (mp0) REVERT: H 113 GLU cc_start: 0.9315 (mm-30) cc_final: 0.9006 (mm-30) outliers start: 10 outliers final: 2 residues processed: 456 average time/residue: 0.3410 time to fit residues: 212.4433 Evaluate side-chains 295 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 292 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 0.0170 chunk 116 optimal weight: 2.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 212 GLN ** O 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 215 GLN G 68 ASN G 89 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS B 93 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN H 63 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.078864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.057822 restraints weight = 82487.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.059152 restraints weight = 43363.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.060029 restraints weight = 28659.969| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15895 Z= 0.217 Angle : 0.638 7.908 22928 Z= 0.378 Chirality : 0.037 0.197 2563 Planarity : 0.006 0.092 1719 Dihedral : 29.984 160.382 4918 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.07 % Favored : 97.61 % Rotamer: Outliers : 0.24 % Allowed : 3.23 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.27), residues: 964 helix: 2.63 (0.20), residues: 624 sheet: -1.83 (0.93), residues: 24 loop : -0.19 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP P 214 HIS 0.003 0.001 HIS D 49 PHE 0.014 0.002 PHE F 100 TYR 0.018 0.002 TYR G 39 ARG 0.011 0.001 ARG O 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 349 time to evaluate : 1.039 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: P 181 MET cc_start: 0.4322 (tpt) cc_final: 0.3577 (mmt) REVERT: G 58 LEU cc_start: 0.9695 (mm) cc_final: 0.9426 (mm) REVERT: G 64 GLU cc_start: 0.9489 (OUTLIER) cc_final: 0.8857 (pp20) REVERT: G 87 ILE cc_start: 0.9560 (mt) cc_final: 0.8993 (tp) REVERT: G 88 ARG cc_start: 0.8885 (mmt180) cc_final: 0.7826 (mtp180) REVERT: G 94 ASN cc_start: 0.9290 (t0) cc_final: 0.9018 (m-40) REVERT: G 100 VAL cc_start: 0.9285 (t) cc_final: 0.8984 (p) REVERT: A 50 GLU cc_start: 0.9437 (mt-10) cc_final: 0.8794 (mt-10) REVERT: A 51 ILE cc_start: 0.8344 (mt) cc_final: 0.8004 (mt) REVERT: A 53 ARG cc_start: 0.9663 (ptm-80) cc_final: 0.9389 (ptm160) REVERT: A 59 GLU cc_start: 0.8303 (pm20) cc_final: 0.8088 (pm20) REVERT: A 73 GLU cc_start: 0.8322 (tt0) cc_final: 0.7875 (tt0) REVERT: A 81 ASP cc_start: 0.8025 (t0) cc_final: 0.7817 (t0) REVERT: A 87 SER cc_start: 0.8852 (p) cc_final: 0.8378 (t) REVERT: A 90 MET cc_start: 0.8916 (mpp) cc_final: 0.8463 (mmm) REVERT: A 94 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8439 (mm-30) REVERT: A 105 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8478 (tm-30) REVERT: A 126 LEU cc_start: 0.9545 (mm) cc_final: 0.9061 (mm) REVERT: B 25 ASN cc_start: 0.7870 (m110) cc_final: 0.7453 (m110) REVERT: B 39 ARG cc_start: 0.9221 (mmt-90) cc_final: 0.8607 (tpp-160) REVERT: B 49 LEU cc_start: 0.9529 (mm) cc_final: 0.9030 (tp) REVERT: B 84 MET cc_start: 0.9396 (mpp) cc_final: 0.9100 (mpp) REVERT: C 50 TYR cc_start: 0.8365 (t80) cc_final: 0.7839 (t80) REVERT: C 74 LYS cc_start: 0.9433 (mmtm) cc_final: 0.9136 (mmtm) REVERT: C 78 ILE cc_start: 0.8517 (mm) cc_final: 0.8236 (tp) REVERT: C 90 ASP cc_start: 0.8535 (t0) cc_final: 0.8259 (t0) REVERT: C 92 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8499 (mt-10) REVERT: D 62 MET cc_start: 0.9072 (mmm) cc_final: 0.8843 (mmm) REVERT: D 85 LYS cc_start: 0.9376 (mtpt) cc_final: 0.9076 (mmmt) REVERT: D 94 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9147 (mt) REVERT: D 101 LEU cc_start: 0.9148 (tt) cc_final: 0.8869 (tt) REVERT: E 48 LEU cc_start: 0.9253 (mt) cc_final: 0.8941 (mt) REVERT: E 50 GLU cc_start: 0.9174 (tp30) cc_final: 0.8961 (mm-30) REVERT: E 70 LEU cc_start: 0.9667 (tp) cc_final: 0.9433 (tp) REVERT: E 74 ILE cc_start: 0.9434 (mt) cc_final: 0.9150 (mt) REVERT: E 77 ASP cc_start: 0.9649 (m-30) cc_final: 0.9408 (m-30) REVERT: E 120 MET cc_start: 0.9030 (mmm) cc_final: 0.8647 (mmm) REVERT: F 44 LYS cc_start: 0.8974 (tptm) cc_final: 0.8627 (tptm) REVERT: F 63 GLU cc_start: 0.9348 (pt0) cc_final: 0.9069 (pp20) REVERT: F 84 MET cc_start: 0.9541 (tpt) cc_final: 0.9183 (tpp) REVERT: H 49 HIS cc_start: 0.8972 (m-70) cc_final: 0.8385 (m-70) REVERT: H 59 MET cc_start: 0.9004 (tpp) cc_final: 0.8775 (tpp) REVERT: H 68 ASP cc_start: 0.8926 (t0) cc_final: 0.8643 (t0) REVERT: H 69 ILE cc_start: 0.9131 (mm) cc_final: 0.8691 (mm) REVERT: H 86 ARG cc_start: 0.9006 (mmt-90) cc_final: 0.8440 (mmm-85) REVERT: H 91 SER cc_start: 0.9040 (p) cc_final: 0.8579 (p) REVERT: H 105 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8789 (mm-30) REVERT: H 109 HIS cc_start: 0.8987 (m-70) cc_final: 0.8345 (m90) REVERT: H 113 GLU cc_start: 0.9465 (mm-30) cc_final: 0.9021 (mm-30) outliers start: 2 outliers final: 0 residues processed: 350 average time/residue: 0.3102 time to fit residues: 152.9822 Evaluate side-chains 274 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 272 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 117 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 209 GLN ** O 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN H 82 HIS ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.072851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.052532 restraints weight = 87254.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.053749 restraints weight = 46009.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.054537 restraints weight = 30325.819| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 15895 Z= 0.373 Angle : 0.729 7.769 22928 Z= 0.426 Chirality : 0.041 0.200 2563 Planarity : 0.007 0.092 1719 Dihedral : 30.473 159.995 4918 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.80 % Favored : 96.89 % Rotamer: Outliers : 0.60 % Allowed : 4.07 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.27), residues: 964 helix: 1.68 (0.20), residues: 630 sheet: -1.86 (0.97), residues: 24 loop : -0.49 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP P 244 HIS 0.008 0.002 HIS F 75 PHE 0.017 0.002 PHE F 61 TYR 0.017 0.002 TYR G 50 ARG 0.009 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 312 time to evaluate : 1.073 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: symmetry clash revert: symmetry clash REVERT: P 181 MET cc_start: 0.4534 (tpt) cc_final: 0.3817 (mmt) REVERT: G 64 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8806 (pp20) REVERT: G 68 ASN cc_start: 0.9618 (m-40) cc_final: 0.9019 (m110) REVERT: G 83 LEU cc_start: 0.9623 (mt) cc_final: 0.9409 (mt) REVERT: G 87 ILE cc_start: 0.9563 (mt) cc_final: 0.9009 (tp) REVERT: G 88 ARG cc_start: 0.8910 (mmt180) cc_final: 0.7780 (mtp180) REVERT: G 100 VAL cc_start: 0.9397 (t) cc_final: 0.9107 (p) REVERT: A 51 ILE cc_start: 0.8520 (mt) cc_final: 0.8189 (mt) REVERT: A 53 ARG cc_start: 0.9523 (ptm-80) cc_final: 0.9253 (ptm160) REVERT: A 54 TYR cc_start: 0.9548 (m-80) cc_final: 0.8686 (m-80) REVERT: A 73 GLU cc_start: 0.8340 (tt0) cc_final: 0.8013 (tt0) REVERT: A 87 SER cc_start: 0.9137 (p) cc_final: 0.8652 (t) REVERT: A 90 MET cc_start: 0.8913 (mpp) cc_final: 0.8423 (mmm) REVERT: A 105 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8495 (tm-30) REVERT: A 120 MET cc_start: 0.8446 (mmt) cc_final: 0.8200 (mmt) REVERT: B 25 ASN cc_start: 0.8001 (m110) cc_final: 0.7701 (m110) REVERT: B 39 ARG cc_start: 0.9124 (mmt-90) cc_final: 0.8634 (tpp-160) REVERT: B 43 VAL cc_start: 0.9245 (t) cc_final: 0.8869 (p) REVERT: B 49 LEU cc_start: 0.9466 (mm) cc_final: 0.8981 (tp) REVERT: B 84 MET cc_start: 0.9376 (mpp) cc_final: 0.9089 (mpp) REVERT: C 74 LYS cc_start: 0.9368 (mmtm) cc_final: 0.9147 (mmtm) REVERT: C 90 ASP cc_start: 0.8504 (t0) cc_final: 0.8238 (t0) REVERT: D 62 MET cc_start: 0.9280 (mmm) cc_final: 0.8740 (mmm) REVERT: D 101 LEU cc_start: 0.9234 (tt) cc_final: 0.8992 (tt) REVERT: E 50 GLU cc_start: 0.9194 (tp30) cc_final: 0.8871 (tp30) REVERT: E 74 ILE cc_start: 0.9474 (mt) cc_final: 0.9220 (mt) REVERT: E 77 ASP cc_start: 0.9601 (m-30) cc_final: 0.9330 (m-30) REVERT: E 90 MET cc_start: 0.9457 (mmp) cc_final: 0.9251 (mmm) REVERT: E 93 GLN cc_start: 0.9058 (tt0) cc_final: 0.8807 (tt0) REVERT: E 119 ILE cc_start: 0.9476 (pt) cc_final: 0.9272 (pt) REVERT: E 120 MET cc_start: 0.8944 (mmm) cc_final: 0.8551 (mmm) REVERT: F 25 ASN cc_start: 0.8525 (m-40) cc_final: 0.7994 (m-40) REVERT: F 63 GLU cc_start: 0.9302 (pt0) cc_final: 0.8925 (pp20) REVERT: F 64 ASN cc_start: 0.9611 (t0) cc_final: 0.9276 (t0) REVERT: F 88 TYR cc_start: 0.9132 (m-10) cc_final: 0.8663 (m-10) REVERT: H 46 LYS cc_start: 0.9433 (ptpp) cc_final: 0.9182 (ptpp) REVERT: H 47 GLN cc_start: 0.9305 (tm-30) cc_final: 0.9027 (tm-30) REVERT: H 49 HIS cc_start: 0.9024 (m-70) cc_final: 0.8630 (m90) REVERT: H 59 MET cc_start: 0.8998 (tpp) cc_final: 0.8512 (tpp) REVERT: H 63 ASN cc_start: 0.9350 (m-40) cc_final: 0.8953 (m110) REVERT: H 82 HIS cc_start: 0.9020 (OUTLIER) cc_final: 0.8593 (m90) REVERT: H 108 LYS cc_start: 0.9292 (ptmm) cc_final: 0.9006 (pttm) REVERT: H 109 HIS cc_start: 0.9057 (m-70) cc_final: 0.8105 (m-70) REVERT: H 113 GLU cc_start: 0.9367 (mm-30) cc_final: 0.8627 (mm-30) outliers start: 5 outliers final: 1 residues processed: 315 average time/residue: 0.3100 time to fit residues: 137.4721 Evaluate side-chains 259 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 256 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 23 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 215 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.075374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.054438 restraints weight = 86183.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.055601 restraints weight = 46750.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.056304 restraints weight = 31765.197| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15895 Z= 0.236 Angle : 0.651 7.993 22928 Z= 0.385 Chirality : 0.038 0.204 2563 Planarity : 0.005 0.093 1719 Dihedral : 30.489 157.969 4918 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.70 % Favored : 97.10 % Rotamer: Outliers : 0.12 % Allowed : 2.99 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.27), residues: 964 helix: 1.64 (0.20), residues: 630 sheet: -1.83 (0.94), residues: 24 loop : -0.45 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP P 244 HIS 0.005 0.001 HIS F 75 PHE 0.017 0.002 PHE D 70 TYR 0.017 0.002 TYR P 207 ARG 0.007 0.001 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 315 time to evaluate : 1.180 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: symmetry clash revert: symmetry clash REVERT: O 201 MET cc_start: 0.7717 (mpp) cc_final: 0.7298 (mpp) REVERT: P 181 MET cc_start: 0.4147 (tpt) cc_final: 0.3631 (mmp) REVERT: G 88 ARG cc_start: 0.8725 (mmt180) cc_final: 0.8511 (mmt180) REVERT: A 50 GLU cc_start: 0.9420 (mt-10) cc_final: 0.8780 (mt-10) REVERT: A 51 ILE cc_start: 0.8437 (mt) cc_final: 0.8159 (mt) REVERT: A 53 ARG cc_start: 0.9506 (ptm-80) cc_final: 0.9269 (ptm160) REVERT: A 54 TYR cc_start: 0.9525 (m-80) cc_final: 0.8987 (m-80) REVERT: A 60 LEU cc_start: 0.9230 (mp) cc_final: 0.8995 (mt) REVERT: A 73 GLU cc_start: 0.8186 (tt0) cc_final: 0.7934 (tt0) REVERT: A 87 SER cc_start: 0.9127 (p) cc_final: 0.8688 (t) REVERT: A 90 MET cc_start: 0.8761 (mpp) cc_final: 0.8432 (mmm) REVERT: A 105 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8392 (tm-30) REVERT: A 106 ASP cc_start: 0.8331 (m-30) cc_final: 0.8106 (m-30) REVERT: A 120 MET cc_start: 0.8416 (mmt) cc_final: 0.8198 (mmt) REVERT: B 39 ARG cc_start: 0.8976 (mmt-90) cc_final: 0.8314 (tpp-160) REVERT: B 43 VAL cc_start: 0.9156 (t) cc_final: 0.8772 (p) REVERT: B 49 LEU cc_start: 0.9455 (mm) cc_final: 0.9009 (tp) REVERT: B 63 GLU cc_start: 0.8661 (pp20) cc_final: 0.8398 (pp20) REVERT: B 84 MET cc_start: 0.9345 (mpp) cc_final: 0.9080 (mpp) REVERT: C 39 TYR cc_start: 0.8932 (m-80) cc_final: 0.8118 (m-80) REVERT: C 74 LYS cc_start: 0.9323 (mmtm) cc_final: 0.9067 (mppt) REVERT: C 75 LYS cc_start: 0.8960 (tptm) cc_final: 0.8510 (tptp) REVERT: C 90 ASP cc_start: 0.8352 (t0) cc_final: 0.8064 (t0) REVERT: D 34 LYS cc_start: 0.8631 (pptt) cc_final: 0.8323 (mmtp) REVERT: D 62 MET cc_start: 0.9072 (mmm) cc_final: 0.8537 (mmm) REVERT: D 68 ASP cc_start: 0.9313 (t0) cc_final: 0.9007 (t0) REVERT: D 101 LEU cc_start: 0.9280 (tt) cc_final: 0.8984 (tt) REVERT: E 50 GLU cc_start: 0.9105 (tp30) cc_final: 0.8665 (tp30) REVERT: E 60 LEU cc_start: 0.9317 (mm) cc_final: 0.8848 (mm) REVERT: E 74 ILE cc_start: 0.9484 (mt) cc_final: 0.9176 (mt) REVERT: E 77 ASP cc_start: 0.9549 (m-30) cc_final: 0.9277 (m-30) REVERT: E 90 MET cc_start: 0.9390 (mmp) cc_final: 0.9154 (mmm) REVERT: E 93 GLN cc_start: 0.8973 (tt0) cc_final: 0.8729 (tt0) REVERT: E 120 MET cc_start: 0.9165 (mmm) cc_final: 0.8518 (mmm) REVERT: F 63 GLU cc_start: 0.9251 (pt0) cc_final: 0.8857 (pp20) REVERT: F 64 ASN cc_start: 0.9585 (t0) cc_final: 0.9279 (t0) REVERT: F 84 MET cc_start: 0.9393 (tpp) cc_final: 0.9130 (tpp) REVERT: H 46 LYS cc_start: 0.9393 (ptpp) cc_final: 0.8657 (ptpp) REVERT: H 47 GLN cc_start: 0.9169 (tm-30) cc_final: 0.8901 (tm-30) REVERT: H 59 MET cc_start: 0.8853 (tpp) cc_final: 0.8476 (tpp) REVERT: H 109 HIS cc_start: 0.9027 (m-70) cc_final: 0.8065 (m-70) REVERT: H 113 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8620 (mm-30) outliers start: 1 outliers final: 0 residues processed: 315 average time/residue: 0.3028 time to fit residues: 134.5658 Evaluate side-chains 258 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 81 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 68 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** 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 = 0.3638 r_free = 0.3638 target = 0.076227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.055663 restraints weight = 84726.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.056922 restraints weight = 45377.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.057781 restraints weight = 30568.727| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15895 Z= 0.203 Angle : 0.630 8.269 22928 Z= 0.375 Chirality : 0.037 0.192 2563 Planarity : 0.005 0.094 1719 Dihedral : 30.379 152.822 4918 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.80 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.27), residues: 964 helix: 1.66 (0.20), residues: 628 sheet: -1.70 (0.97), residues: 24 loop : -0.40 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 214 HIS 0.005 0.001 HIS F 75 PHE 0.014 0.001 PHE D 70 TYR 0.017 0.002 TYR H 40 ARG 0.010 0.000 ARG O 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 1.256 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: symmetry clash revert: symmetry clash REVERT: O 201 MET cc_start: 0.7679 (mpp) cc_final: 0.7142 (mpp) REVERT: P 181 MET cc_start: 0.4162 (tpt) cc_final: 0.3599 (mmp) REVERT: G 38 ASN cc_start: 0.9187 (t0) cc_final: 0.8985 (t0) REVERT: G 39 TYR cc_start: 0.8818 (m-80) cc_final: 0.8597 (m-80) REVERT: G 56 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8667 (tm-30) REVERT: G 68 ASN cc_start: 0.9560 (m-40) cc_final: 0.9348 (m110) REVERT: G 88 ARG cc_start: 0.8779 (mmt180) cc_final: 0.8574 (mmt180) REVERT: A 50 GLU cc_start: 0.9429 (mt-10) cc_final: 0.8995 (mt-10) REVERT: A 53 ARG cc_start: 0.9463 (ptm-80) cc_final: 0.9251 (ptm160) REVERT: A 54 TYR cc_start: 0.9412 (m-80) cc_final: 0.8930 (m-80) REVERT: A 87 SER cc_start: 0.9073 (p) cc_final: 0.8621 (t) REVERT: A 90 MET cc_start: 0.8850 (mpp) cc_final: 0.8452 (mmm) REVERT: A 105 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8427 (tm-30) REVERT: A 130 ILE cc_start: 0.9379 (mm) cc_final: 0.9096 (mm) REVERT: B 45 ARG cc_start: 0.8912 (mmm-85) cc_final: 0.8629 (mmm160) REVERT: B 49 LEU cc_start: 0.9453 (mm) cc_final: 0.8999 (tp) REVERT: B 63 GLU cc_start: 0.8721 (pp20) cc_final: 0.8434 (pp20) REVERT: B 84 MET cc_start: 0.9392 (mpp) cc_final: 0.9115 (mpp) REVERT: C 39 TYR cc_start: 0.8731 (m-80) cc_final: 0.8179 (m-80) REVERT: C 74 LYS cc_start: 0.9287 (mmtm) cc_final: 0.9062 (mppt) REVERT: C 90 ASP cc_start: 0.8347 (t0) cc_final: 0.8069 (t0) REVERT: D 83 TYR cc_start: 0.8357 (m-10) cc_final: 0.7569 (m-10) REVERT: D 85 LYS cc_start: 0.9459 (mtpt) cc_final: 0.9032 (mmmt) REVERT: E 50 GLU cc_start: 0.9074 (tp30) cc_final: 0.8665 (tp30) REVERT: E 60 LEU cc_start: 0.9219 (mm) cc_final: 0.8906 (mm) REVERT: E 74 ILE cc_start: 0.9485 (mt) cc_final: 0.9190 (mt) REVERT: E 77 ASP cc_start: 0.9521 (m-30) cc_final: 0.9239 (m-30) REVERT: E 82 LEU cc_start: 0.7705 (mt) cc_final: 0.7446 (mt) REVERT: E 90 MET cc_start: 0.9417 (mmp) cc_final: 0.9187 (mmm) REVERT: E 93 GLN cc_start: 0.8893 (tt0) cc_final: 0.8658 (tt0) REVERT: E 120 MET cc_start: 0.9161 (mmm) cc_final: 0.8397 (mmm) REVERT: E 126 LEU cc_start: 0.9170 (mm) cc_final: 0.8826 (tp) REVERT: F 63 GLU cc_start: 0.9243 (pt0) cc_final: 0.8824 (pp20) REVERT: F 64 ASN cc_start: 0.9603 (t0) cc_final: 0.9292 (t0) REVERT: F 84 MET cc_start: 0.9346 (tpp) cc_final: 0.9136 (tpp) REVERT: H 47 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8908 (tm-30) REVERT: H 49 HIS cc_start: 0.8578 (m90) cc_final: 0.8294 (m-70) REVERT: H 76 GLU cc_start: 0.8833 (mp0) cc_final: 0.8457 (mp0) REVERT: H 109 HIS cc_start: 0.8976 (m-70) cc_final: 0.8090 (m-70) REVERT: H 113 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8629 (mm-30) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.3183 time to fit residues: 140.4448 Evaluate side-chains 266 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 75 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 122 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 215 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS D 109 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.077484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.056797 restraints weight = 85699.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.057957 restraints weight = 45355.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.058722 restraints weight = 30478.094| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15895 Z= 0.183 Angle : 0.625 8.339 22928 Z= 0.370 Chirality : 0.036 0.183 2563 Planarity : 0.005 0.094 1719 Dihedral : 30.286 150.164 4918 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.80 % Favored : 96.99 % Rotamer: Outliers : 0.12 % Allowed : 2.04 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.27), residues: 964 helix: 1.66 (0.20), residues: 628 sheet: -1.76 (0.95), residues: 24 loop : -0.41 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 214 HIS 0.003 0.001 HIS F 75 PHE 0.014 0.001 PHE D 65 TYR 0.022 0.001 TYR O 259 ARG 0.006 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 316 time to evaluate : 1.162 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: O 201 MET cc_start: 0.7875 (mpp) cc_final: 0.7511 (mpp) REVERT: P 181 MET cc_start: 0.4195 (tpt) cc_final: 0.3646 (mmt) REVERT: G 56 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8567 (tm-30) REVERT: G 68 ASN cc_start: 0.9549 (m-40) cc_final: 0.9045 (m110) REVERT: G 82 HIS cc_start: 0.8333 (m170) cc_final: 0.8016 (m90) REVERT: G 88 ARG cc_start: 0.8705 (mmt180) cc_final: 0.8353 (mmt180) REVERT: A 50 GLU cc_start: 0.9433 (mt-10) cc_final: 0.9004 (mt-10) REVERT: A 53 ARG cc_start: 0.9465 (ptm-80) cc_final: 0.9212 (ptm160) REVERT: A 54 TYR cc_start: 0.9404 (m-80) cc_final: 0.8975 (m-80) REVERT: A 73 GLU cc_start: 0.8214 (tt0) cc_final: 0.7979 (tt0) REVERT: A 87 SER cc_start: 0.8871 (p) cc_final: 0.8424 (t) REVERT: A 90 MET cc_start: 0.8888 (mpp) cc_final: 0.8544 (mmm) REVERT: A 105 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8402 (tm-30) REVERT: B 49 LEU cc_start: 0.9478 (mm) cc_final: 0.8864 (tp) REVERT: B 52 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8599 (mp0) REVERT: B 63 GLU cc_start: 0.8699 (pp20) cc_final: 0.8415 (pp20) REVERT: C 39 TYR cc_start: 0.8718 (m-80) cc_final: 0.8246 (m-80) REVERT: C 74 LYS cc_start: 0.9314 (mmtm) cc_final: 0.9088 (mppt) REVERT: C 90 ASP cc_start: 0.8358 (t0) cc_final: 0.7962 (t0) REVERT: D 85 LYS cc_start: 0.9446 (mtpt) cc_final: 0.9018 (mmmt) REVERT: D 96 THR cc_start: 0.9542 (m) cc_final: 0.9332 (p) REVERT: E 50 GLU cc_start: 0.9053 (tp30) cc_final: 0.8593 (tp30) REVERT: E 60 LEU cc_start: 0.9083 (mm) cc_final: 0.8853 (mm) REVERT: E 74 ILE cc_start: 0.9470 (mt) cc_final: 0.9173 (mt) REVERT: E 77 ASP cc_start: 0.9487 (m-30) cc_final: 0.9225 (m-30) REVERT: E 82 LEU cc_start: 0.7605 (mt) cc_final: 0.7323 (mt) REVERT: E 90 MET cc_start: 0.9402 (mmp) cc_final: 0.9151 (mmm) REVERT: E 120 MET cc_start: 0.9041 (mmm) cc_final: 0.8484 (mmm) REVERT: F 49 LEU cc_start: 0.9453 (mt) cc_final: 0.9125 (mt) REVERT: F 63 GLU cc_start: 0.9262 (pt0) cc_final: 0.8849 (pp20) REVERT: F 64 ASN cc_start: 0.9600 (t0) cc_final: 0.9296 (t0) REVERT: H 59 MET cc_start: 0.8709 (tpp) cc_final: 0.8392 (tpp) REVERT: H 69 ILE cc_start: 0.8877 (mm) cc_final: 0.8533 (mm) REVERT: H 86 ARG cc_start: 0.8888 (mmt-90) cc_final: 0.8599 (mmm-85) REVERT: H 109 HIS cc_start: 0.8971 (m-70) cc_final: 0.8053 (m-70) REVERT: H 113 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8596 (mm-30) outliers start: 1 outliers final: 0 residues processed: 317 average time/residue: 0.2956 time to fit residues: 133.4287 Evaluate side-chains 258 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 63 optimal weight: 4.9990 chunk 94 optimal weight: 0.1980 chunk 47 optimal weight: 5.9990 chunk 111 optimal weight: 0.4980 chunk 66 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 44 optimal weight: 0.0770 chunk 6 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** F 75 HIS ** 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 = 0.3639 r_free = 0.3639 target = 0.075965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.055252 restraints weight = 87530.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.056422 restraints weight = 46962.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.057186 restraints weight = 31851.173| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15895 Z= 0.220 Angle : 0.652 10.532 22928 Z= 0.382 Chirality : 0.037 0.248 2563 Planarity : 0.006 0.112 1719 Dihedral : 30.326 150.509 4918 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.01 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.27), residues: 964 helix: 1.56 (0.20), residues: 626 sheet: -1.70 (0.98), residues: 24 loop : -0.55 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 214 HIS 0.009 0.001 HIS D 109 PHE 0.023 0.002 PHE F 61 TYR 0.017 0.002 TYR H 40 ARG 0.006 0.000 ARG O 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.076 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: O 201 MET cc_start: 0.7820 (mpp) cc_final: 0.7403 (mpp) REVERT: P 181 MET cc_start: 0.4222 (tpt) cc_final: 0.3636 (mmt) REVERT: G 39 TYR cc_start: 0.8692 (m-80) cc_final: 0.8389 (m-80) REVERT: G 56 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8545 (tm-30) REVERT: G 68 ASN cc_start: 0.9427 (m-40) cc_final: 0.9204 (m110) REVERT: A 50 GLU cc_start: 0.9456 (mt-10) cc_final: 0.9012 (mt-10) REVERT: A 53 ARG cc_start: 0.9464 (ptm-80) cc_final: 0.9245 (ptm160) REVERT: A 54 TYR cc_start: 0.9435 (m-80) cc_final: 0.8997 (m-80) REVERT: A 87 SER cc_start: 0.8928 (p) cc_final: 0.8467 (t) REVERT: A 90 MET cc_start: 0.8891 (mpp) cc_final: 0.8536 (mmm) REVERT: A 105 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8438 (tm-30) REVERT: A 120 MET cc_start: 0.8722 (mmt) cc_final: 0.8501 (mmt) REVERT: A 126 LEU cc_start: 0.9768 (tp) cc_final: 0.9532 (mm) REVERT: B 31 LYS cc_start: 0.9479 (pptt) cc_final: 0.9271 (ptmm) REVERT: B 49 LEU cc_start: 0.9439 (mm) cc_final: 0.8836 (tp) REVERT: B 63 GLU cc_start: 0.8747 (pp20) cc_final: 0.8464 (pp20) REVERT: B 64 ASN cc_start: 0.8805 (t0) cc_final: 0.8551 (t0) REVERT: C 74 LYS cc_start: 0.9300 (mmtm) cc_final: 0.9097 (mppt) REVERT: C 90 ASP cc_start: 0.8467 (t0) cc_final: 0.8073 (t0) REVERT: D 85 LYS cc_start: 0.9461 (mtpt) cc_final: 0.9034 (mmmt) REVERT: E 50 GLU cc_start: 0.9050 (tp30) cc_final: 0.8605 (tp30) REVERT: E 74 ILE cc_start: 0.9475 (mt) cc_final: 0.9162 (mt) REVERT: E 77 ASP cc_start: 0.9491 (m-30) cc_final: 0.9238 (m-30) REVERT: E 82 LEU cc_start: 0.7707 (mt) cc_final: 0.7314 (mt) REVERT: E 90 MET cc_start: 0.9390 (mmp) cc_final: 0.9176 (mmm) REVERT: E 93 GLN cc_start: 0.8832 (tt0) cc_final: 0.8534 (tt0) REVERT: E 119 ILE cc_start: 0.9462 (pt) cc_final: 0.9226 (pt) REVERT: E 120 MET cc_start: 0.8974 (mmm) cc_final: 0.8417 (mmm) REVERT: F 49 LEU cc_start: 0.9454 (mt) cc_final: 0.9244 (mt) REVERT: F 63 GLU cc_start: 0.9247 (pt0) cc_final: 0.8800 (pp20) REVERT: F 64 ASN cc_start: 0.9588 (t0) cc_final: 0.9277 (t0) REVERT: F 84 MET cc_start: 0.9339 (tpt) cc_final: 0.9096 (tpp) REVERT: F 88 TYR cc_start: 0.8951 (m-10) cc_final: 0.8427 (m-80) REVERT: H 34 LYS cc_start: 0.9046 (mmmm) cc_final: 0.8785 (mptt) REVERT: H 69 ILE cc_start: 0.8872 (mm) cc_final: 0.8499 (mm) REVERT: H 86 ARG cc_start: 0.8853 (mmt-90) cc_final: 0.8517 (mmm-85) REVERT: H 109 HIS cc_start: 0.8991 (m-70) cc_final: 0.8116 (m-70) REVERT: H 113 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8580 (mm-30) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.2933 time to fit residues: 129.2115 Evaluate side-chains 253 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 61 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 60 optimal weight: 0.0670 chunk 70 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.076864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.056141 restraints weight = 86989.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.057284 restraints weight = 47005.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.058058 restraints weight = 32004.979| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15895 Z= 0.197 Angle : 0.644 10.791 22928 Z= 0.378 Chirality : 0.037 0.249 2563 Planarity : 0.005 0.095 1719 Dihedral : 30.302 149.636 4918 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.70 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.27), residues: 964 helix: 1.50 (0.20), residues: 628 sheet: -1.62 (0.98), residues: 24 loop : -0.47 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP O 214 HIS 0.007 0.001 HIS F 75 PHE 0.016 0.001 PHE D 65 TYR 0.023 0.001 TYR H 40 ARG 0.008 0.000 ARG O 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 1.085 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: O 201 MET cc_start: 0.7804 (mpp) cc_final: 0.7569 (mpp) REVERT: P 181 MET cc_start: 0.4205 (tpt) cc_final: 0.3632 (mmt) REVERT: G 39 TYR cc_start: 0.8690 (m-80) cc_final: 0.8328 (m-80) REVERT: G 56 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8457 (tm-30) REVERT: G 68 ASN cc_start: 0.9410 (m-40) cc_final: 0.9136 (m110) REVERT: A 50 GLU cc_start: 0.9437 (mt-10) cc_final: 0.9019 (mt-10) REVERT: A 53 ARG cc_start: 0.9483 (ptm-80) cc_final: 0.9248 (ptm160) REVERT: A 54 TYR cc_start: 0.9406 (m-80) cc_final: 0.9030 (m-80) REVERT: A 70 LEU cc_start: 0.9262 (tt) cc_final: 0.8778 (pp) REVERT: A 87 SER cc_start: 0.8901 (p) cc_final: 0.8442 (t) REVERT: A 90 MET cc_start: 0.8892 (mpp) cc_final: 0.8524 (mmm) REVERT: A 94 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8042 (mt-10) REVERT: A 120 MET cc_start: 0.8776 (mmt) cc_final: 0.8282 (mmm) REVERT: A 126 LEU cc_start: 0.9748 (tp) cc_final: 0.9528 (mm) REVERT: B 49 LEU cc_start: 0.9357 (mm) cc_final: 0.9059 (tp) REVERT: B 63 GLU cc_start: 0.8722 (pp20) cc_final: 0.8490 (pp20) REVERT: C 36 LYS cc_start: 0.9398 (mmtm) cc_final: 0.8986 (mtmt) REVERT: C 90 ASP cc_start: 0.8491 (t0) cc_final: 0.8142 (t0) REVERT: D 85 LYS cc_start: 0.9459 (mtpt) cc_final: 0.9030 (mmmt) REVERT: D 116 LYS cc_start: 0.9323 (mtmm) cc_final: 0.9014 (ptpp) REVERT: E 50 GLU cc_start: 0.9038 (tp30) cc_final: 0.8574 (tp30) REVERT: E 77 ASP cc_start: 0.9484 (m-30) cc_final: 0.9231 (m-30) REVERT: E 82 LEU cc_start: 0.7728 (mt) cc_final: 0.7340 (mt) REVERT: E 90 MET cc_start: 0.9352 (mmp) cc_final: 0.9093 (mmm) REVERT: E 93 GLN cc_start: 0.8812 (tt0) cc_final: 0.8600 (tt0) REVERT: E 106 ASP cc_start: 0.9023 (m-30) cc_final: 0.8606 (m-30) REVERT: E 119 ILE cc_start: 0.9481 (pt) cc_final: 0.9267 (pt) REVERT: E 120 MET cc_start: 0.8930 (mmm) cc_final: 0.8329 (mmm) REVERT: F 44 LYS cc_start: 0.8591 (tppt) cc_final: 0.8381 (tppt) REVERT: F 49 LEU cc_start: 0.9429 (mt) cc_final: 0.9080 (mt) REVERT: F 63 GLU cc_start: 0.9248 (pt0) cc_final: 0.8809 (pp20) REVERT: F 64 ASN cc_start: 0.9581 (t0) cc_final: 0.9280 (t0) REVERT: F 66 ILE cc_start: 0.9640 (mm) cc_final: 0.9266 (mt) REVERT: H 59 MET cc_start: 0.8759 (tpp) cc_final: 0.8467 (tpt) REVERT: H 69 ILE cc_start: 0.8827 (mm) cc_final: 0.8469 (mm) REVERT: H 76 GLU cc_start: 0.8856 (mp0) cc_final: 0.8651 (mp0) REVERT: H 86 ARG cc_start: 0.8982 (mmt-90) cc_final: 0.8501 (mmm-85) REVERT: H 105 GLU cc_start: 0.8401 (pm20) cc_final: 0.8068 (pm20) REVERT: H 108 LYS cc_start: 0.8927 (pttm) cc_final: 0.8674 (pptt) REVERT: H 109 HIS cc_start: 0.8989 (m-70) cc_final: 0.8776 (t-170) REVERT: H 113 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8418 (mm-30) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.2828 time to fit residues: 122.4424 Evaluate side-chains 252 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 111 optimal weight: 0.0870 chunk 44 optimal weight: 0.0000 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 overall best weight: 0.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 220 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** 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 = 0.3691 r_free = 0.3691 target = 0.078527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.057691 restraints weight = 85850.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.058884 restraints weight = 46633.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.059665 restraints weight = 31968.053| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15895 Z= 0.180 Angle : 0.640 10.771 22928 Z= 0.374 Chirality : 0.036 0.191 2563 Planarity : 0.005 0.095 1719 Dihedral : 30.160 149.276 4918 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.32 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.27), residues: 964 helix: 1.52 (0.20), residues: 620 sheet: -1.51 (1.00), residues: 24 loop : -0.44 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 214 HIS 0.008 0.001 HIS B 75 PHE 0.021 0.001 PHE F 61 TYR 0.021 0.001 TYR H 40 ARG 0.004 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 1.114 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: O 201 MET cc_start: 0.8061 (mpp) cc_final: 0.7647 (mpp) REVERT: P 181 MET cc_start: 0.4213 (tpt) cc_final: 0.3628 (mmt) REVERT: G 11 ARG cc_start: 0.7200 (tpp80) cc_final: 0.6209 (mmm160) REVERT: G 39 TYR cc_start: 0.8637 (m-80) cc_final: 0.8379 (m-80) REVERT: G 56 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8371 (tm-30) REVERT: G 68 ASN cc_start: 0.9415 (m-40) cc_final: 0.9140 (m110) REVERT: G 107 VAL cc_start: 0.8911 (m) cc_final: 0.8613 (p) REVERT: A 50 GLU cc_start: 0.9424 (mt-10) cc_final: 0.9010 (mt-10) REVERT: A 53 ARG cc_start: 0.9427 (ptm-80) cc_final: 0.9178 (ptm160) REVERT: A 54 TYR cc_start: 0.9437 (m-80) cc_final: 0.9067 (m-80) REVERT: A 70 LEU cc_start: 0.9268 (tt) cc_final: 0.8806 (pp) REVERT: A 73 GLU cc_start: 0.8038 (tt0) cc_final: 0.7789 (tt0) REVERT: A 87 SER cc_start: 0.8823 (p) cc_final: 0.8309 (t) REVERT: A 90 MET cc_start: 0.8962 (mpp) cc_final: 0.8592 (mmm) REVERT: A 94 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8074 (mt-10) REVERT: A 120 MET cc_start: 0.8801 (mmt) cc_final: 0.8109 (mmm) REVERT: B 49 LEU cc_start: 0.9504 (mm) cc_final: 0.8835 (tp) REVERT: B 63 GLU cc_start: 0.8702 (pp20) cc_final: 0.8474 (pp20) REVERT: C 36 LYS cc_start: 0.9391 (mmtm) cc_final: 0.9001 (mtmt) REVERT: C 51 LEU cc_start: 0.9629 (tp) cc_final: 0.9419 (tp) REVERT: C 90 ASP cc_start: 0.8402 (t0) cc_final: 0.7854 (t0) REVERT: D 85 LYS cc_start: 0.9438 (mtpt) cc_final: 0.8997 (mmmt) REVERT: E 50 GLU cc_start: 0.9039 (tp30) cc_final: 0.8581 (tp30) REVERT: E 77 ASP cc_start: 0.9434 (m-30) cc_final: 0.9208 (m-30) REVERT: E 82 LEU cc_start: 0.7651 (mt) cc_final: 0.7297 (mt) REVERT: E 90 MET cc_start: 0.9367 (mmp) cc_final: 0.9128 (mmm) REVERT: E 93 GLN cc_start: 0.8831 (tt0) cc_final: 0.8620 (tt0) REVERT: E 106 ASP cc_start: 0.9038 (m-30) cc_final: 0.8549 (m-30) REVERT: E 120 MET cc_start: 0.8906 (mmm) cc_final: 0.8371 (mmm) REVERT: F 44 LYS cc_start: 0.8563 (tppt) cc_final: 0.8325 (tppt) REVERT: F 49 LEU cc_start: 0.9424 (mt) cc_final: 0.9040 (mt) REVERT: F 63 GLU cc_start: 0.9279 (pt0) cc_final: 0.8794 (pp20) REVERT: F 64 ASN cc_start: 0.9554 (t0) cc_final: 0.9234 (t0) REVERT: F 66 ILE cc_start: 0.9615 (mm) cc_final: 0.9149 (mt) REVERT: F 84 MET cc_start: 0.8896 (tpt) cc_final: 0.8672 (tpp) REVERT: H 34 LYS cc_start: 0.9064 (mmmm) cc_final: 0.8814 (mptt) REVERT: H 59 MET cc_start: 0.8768 (tpp) cc_final: 0.8528 (tpp) REVERT: H 69 ILE cc_start: 0.8788 (mm) cc_final: 0.8460 (mm) REVERT: H 71 GLU cc_start: 0.8989 (tp30) cc_final: 0.8765 (tp30) REVERT: H 76 GLU cc_start: 0.8995 (mp0) cc_final: 0.8553 (mp0) REVERT: H 86 ARG cc_start: 0.8973 (mmt-90) cc_final: 0.8470 (ttm-80) REVERT: H 105 GLU cc_start: 0.8396 (pm20) cc_final: 0.8070 (pm20) REVERT: H 108 LYS cc_start: 0.8927 (pttm) cc_final: 0.8592 (pptt) REVERT: H 109 HIS cc_start: 0.8939 (m-70) cc_final: 0.8722 (t-170) REVERT: H 113 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8442 (mm-30) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.3051 time to fit residues: 130.2187 Evaluate side-chains 248 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 114 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** 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 = 0.3578 r_free = 0.3578 target = 0.072914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.052231 restraints weight = 90579.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.053289 restraints weight = 50000.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.053980 restraints weight = 34727.626| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.5885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 15895 Z= 0.314 Angle : 0.716 10.486 22928 Z= 0.417 Chirality : 0.040 0.187 2563 Planarity : 0.006 0.096 1719 Dihedral : 30.607 151.315 4918 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.73 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.27), residues: 964 helix: 1.36 (0.20), residues: 626 sheet: -1.78 (0.99), residues: 24 loop : -0.63 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP P 244 HIS 0.007 0.002 HIS B 75 PHE 0.016 0.002 PHE D 65 TYR 0.022 0.002 TYR H 40 ARG 0.012 0.001 ARG O 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 1.081 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: O 201 MET cc_start: 0.7837 (mpp) cc_final: 0.7364 (mpp) REVERT: G 11 ARG cc_start: 0.8029 (tpp80) cc_final: 0.6799 (tpp80) REVERT: A 50 GLU cc_start: 0.9375 (mt-10) cc_final: 0.9009 (tt0) REVERT: A 53 ARG cc_start: 0.9502 (ptm-80) cc_final: 0.9200 (ptm160) REVERT: A 54 TYR cc_start: 0.9494 (m-80) cc_final: 0.8588 (m-80) REVERT: A 61 LEU cc_start: 0.8619 (mt) cc_final: 0.8354 (mt) REVERT: A 62 ILE cc_start: 0.9216 (tp) cc_final: 0.8970 (pt) REVERT: A 87 SER cc_start: 0.9136 (p) cc_final: 0.8640 (t) REVERT: A 94 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8114 (mm-30) REVERT: A 105 GLU cc_start: 0.8542 (tt0) cc_final: 0.8261 (pp20) REVERT: A 120 MET cc_start: 0.8690 (mmt) cc_final: 0.8455 (mmt) REVERT: B 43 VAL cc_start: 0.9193 (t) cc_final: 0.8699 (p) REVERT: B 63 GLU cc_start: 0.8719 (pp20) cc_final: 0.8490 (pp20) REVERT: B 68 ASP cc_start: 0.8964 (m-30) cc_final: 0.8739 (m-30) REVERT: B 93 GLN cc_start: 0.8459 (pp30) cc_final: 0.8219 (pp30) REVERT: C 36 LYS cc_start: 0.9374 (mmtm) cc_final: 0.9047 (mtmt) REVERT: C 84 GLN cc_start: 0.9055 (tp-100) cc_final: 0.8851 (tp-100) REVERT: C 90 ASP cc_start: 0.8670 (t0) cc_final: 0.8405 (t0) REVERT: D 85 LYS cc_start: 0.9477 (mtpt) cc_final: 0.9050 (mmmt) REVERT: D 96 THR cc_start: 0.9476 (p) cc_final: 0.9250 (p) REVERT: E 50 GLU cc_start: 0.9054 (tp30) cc_final: 0.8542 (tp30) REVERT: E 77 ASP cc_start: 0.9378 (m-30) cc_final: 0.9154 (m-30) REVERT: E 93 GLN cc_start: 0.9019 (tt0) cc_final: 0.8632 (tt0) REVERT: E 106 ASP cc_start: 0.9004 (m-30) cc_final: 0.8653 (m-30) REVERT: E 120 MET cc_start: 0.8968 (mmm) cc_final: 0.8508 (mmm) REVERT: E 125 GLN cc_start: 0.9251 (mt0) cc_final: 0.8749 (mt0) REVERT: F 60 VAL cc_start: 0.9565 (t) cc_final: 0.9210 (t) REVERT: F 63 GLU cc_start: 0.9262 (pt0) cc_final: 0.8788 (pp20) REVERT: F 64 ASN cc_start: 0.9563 (t0) cc_final: 0.9261 (t0) REVERT: F 66 ILE cc_start: 0.9654 (mm) cc_final: 0.9278 (mt) REVERT: F 84 MET cc_start: 0.8913 (tpt) cc_final: 0.8697 (tpp) REVERT: F 88 TYR cc_start: 0.8912 (m-10) cc_final: 0.8149 (m-80) REVERT: H 59 MET cc_start: 0.8682 (tpp) cc_final: 0.8185 (tpp) REVERT: H 69 ILE cc_start: 0.8879 (mm) cc_final: 0.8505 (mm) REVERT: H 86 ARG cc_start: 0.8988 (mmt-90) cc_final: 0.8598 (ttm-80) REVERT: H 109 HIS cc_start: 0.9014 (m-70) cc_final: 0.8160 (m-70) REVERT: H 113 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8602 (mm-30) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.3027 time to fit residues: 121.0827 Evaluate side-chains 237 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 107 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** 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 = 0.3631 r_free = 0.3631 target = 0.075605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.054776 restraints weight = 88255.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.055891 restraints weight = 48643.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.056622 restraints weight = 33345.128| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.5905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15895 Z= 0.206 Angle : 0.666 9.811 22928 Z= 0.386 Chirality : 0.037 0.200 2563 Planarity : 0.005 0.095 1719 Dihedral : 30.439 150.610 4918 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.42 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.27), residues: 964 helix: 1.43 (0.20), residues: 628 sheet: -1.37 (1.06), residues: 24 loop : -0.58 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP O 214 HIS 0.006 0.001 HIS B 75 PHE 0.014 0.001 PHE E 67 TYR 0.023 0.002 TYR H 40 ARG 0.005 0.000 ARG P 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4735.64 seconds wall clock time: 86 minutes 46.79 seconds (5206.79 seconds total)