Starting phenix.real_space_refine on Thu Sep 18 06:20:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vfz_43195/09_2025/8vfz_43195.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vfz_43195/09_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_43195/09_2025/8vfz_43195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vfz_43195/09_2025/8vfz_43195.map" model { file = "/net/cci-nas-00/data/ceres_data/8vfz_43195/09_2025/8vfz_43195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vfz_43195/09_2025/8vfz_43195.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.22, per 1000 atoms: 0.22 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: 1.26 Conformation dependent library (CDL) restraints added in 431.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.57 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: 2.99 Time building geometry restraints manager: 1.71 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.240 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.140 ------------------------------------------------------------------------------- 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= 0.205 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG O 265 TYR 0.007 0.001 TYR B 72 PHE 0.008 0.001 PHE P 224 TRP 0.013 0.002 TRP P 214 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00471 (15895) covalent geometry : angle 0.67647 (22928) hydrogen bonds : bond 0.09641 ( 895) hydrogen bonds : angle 3.61872 ( 2235) *********************** 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 : 0.415 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: 0.3683 (tt) REVERT: P 175 TYR cc_start: 0.4490 (m-80) cc_final: 0.3495 (m-10) REVERT: G 23 LEU cc_start: 0.9433 (mt) cc_final: 0.9049 (mp) REVERT: G 24 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8073 (mm-40) REVERT: G 34 LEU cc_start: 0.9645 (mt) cc_final: 0.9436 (mt) REVERT: G 50 TYR cc_start: 0.8592 (t80) cc_final: 0.8384 (t80) REVERT: G 83 LEU cc_start: 0.9576 (mt) cc_final: 0.9324 (mt) REVERT: G 84 GLN cc_start: 0.9004 (tp40) cc_final: 0.8797 (tp-100) REVERT: G 87 ILE cc_start: 0.9571 (mt) cc_final: 0.9291 (tp) REVERT: G 88 ARG cc_start: 0.8798 (mmt180) cc_final: 0.7981 (mtp180) REVERT: G 100 VAL cc_start: 0.9270 (t) cc_final: 0.8999 (p) REVERT: A 50 GLU cc_start: 0.9388 (mt-10) cc_final: 0.8788 (mt-10) REVERT: A 51 ILE cc_start: 0.8280 (mt) cc_final: 0.7994 (mt) REVERT: A 54 TYR cc_start: 0.9282 (m-80) cc_final: 0.8643 (m-80) REVERT: A 92 LEU cc_start: 0.8900 (mt) cc_final: 0.8687 (mt) REVERT: A 101 VAL cc_start: 0.9237 (t) cc_final: 0.8985 (t) REVERT: A 105 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8504 (tm-30) REVERT: B 39 ARG cc_start: 0.9188 (mmt-90) cc_final: 0.8427 (tpp-160) REVERT: B 68 ASP cc_start: 0.8814 (m-30) cc_final: 0.8498 (m-30) REVERT: B 70 VAL cc_start: 0.9680 (t) cc_final: 0.9342 (m) REVERT: B 87 VAL cc_start: 0.9811 (t) cc_final: 0.9590 (t) REVERT: B 91 LYS cc_start: 0.9690 (ttpt) cc_final: 0.9214 (ptmm) REVERT: C 38 ASN cc_start: 0.8671 (m110) cc_final: 0.8305 (t0) REVERT: C 50 TYR cc_start: 0.8243 (t80) cc_final: 0.8002 (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: 0.8564 (t0) REVERT: C 92 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8289 (mt-10) REVERT: D 62 MET cc_start: 0.9190 (mmm) cc_final: 0.8917 (mmm) REVERT: D 85 LYS cc_start: 0.9370 (mtpt) cc_final: 0.9058 (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: 0.9187 (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: 0.7993 (mp) REVERT: E 93 GLN cc_start: 0.9059 (tt0) cc_final: 0.8248 (tm-30) REVERT: E 109 LEU cc_start: 0.9646 (mt) cc_final: 0.9151 (mm) REVERT: E 125 GLN cc_start: 0.9266 (mt0) cc_final: 0.8877 (mp10) REVERT: F 64 ASN cc_start: 0.9122 (m-40) cc_final: 0.8448 (m110) REVERT: F 68 ASP cc_start: 0.8909 (m-30) cc_final: 0.8702 (m-30) REVERT: F 84 MET cc_start: 0.9140 (mmm) cc_final: 0.8935 (tpp) REVERT: F 85 ASP cc_start: 0.9098 (m-30) cc_final: 0.8802 (t0) REVERT: F 91 LYS cc_start: 0.9430 (ttpt) cc_final: 0.9110 (ptpt) REVERT: H 38 SER cc_start: 0.9131 (m) cc_final: 0.8656 (p) REVERT: H 68 ASP cc_start: 0.8760 (t0) cc_final: 0.8482 (t0) REVERT: H 90 THR cc_start: 0.8750 (p) cc_final: 0.8212 (p) REVERT: H 93 GLU cc_start: 0.8666 (mp0) cc_final: 0.8337 (mp0) REVERT: H 113 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8787 (mm-30) outliers start: 10 outliers final: 2 residues processed: 456 average time/residue: 0.1628 time to fit residues: 101.9237 Evaluate side-chains 293 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 290 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.076289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.054882 restraints weight = 85830.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.056088 restraints weight = 45718.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.056911 restraints weight = 30529.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.057510 restraints weight = 24097.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.057863 restraints weight = 20798.125| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15895 Z= 0.230 Angle : 0.673 8.353 22928 Z= 0.398 Chirality : 0.039 0.210 2563 Planarity : 0.006 0.092 1719 Dihedral : 30.131 161.151 4918 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.28 % Favored : 97.41 % Rotamer: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.27), residues: 964 helix: 2.44 (0.20), residues: 626 sheet: -1.77 (0.97), residues: 24 loop : -0.32 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 86 TYR 0.019 0.002 TYR B 88 PHE 0.014 0.002 PHE F 100 TRP 0.024 0.003 TRP P 214 HIS 0.007 0.001 HIS P 220 Details of bonding type rmsd covalent geometry : bond 0.00505 (15895) covalent geometry : angle 0.67275 (22928) hydrogen bonds : bond 0.05467 ( 895) hydrogen bonds : angle 3.38393 ( 2235) *********************** 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 340 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 339 time to evaluate : 0.417 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 215 GLN cc_start: 0.9442 (pt0) cc_final: 0.9225 (pt0) REVERT: P 181 MET cc_start: 0.4397 (tpt) cc_final: 0.3548 (mmt) REVERT: G 64 GLU cc_start: 0.9505 (OUTLIER) cc_final: 0.8868 (pp20) REVERT: G 84 GLN cc_start: 0.8977 (tp40) cc_final: 0.8538 (tp-100) REVERT: G 87 ILE cc_start: 0.9559 (mt) cc_final: 0.8907 (tp) REVERT: G 88 ARG cc_start: 0.8805 (mmt180) cc_final: 0.7548 (mtp180) REVERT: G 94 ASN cc_start: 0.9303 (t0) cc_final: 0.9026 (m-40) REVERT: G 100 VAL cc_start: 0.9299 (t) cc_final: 0.8827 (p) REVERT: A 50 GLU cc_start: 0.9422 (mt-10) cc_final: 0.8696 (mt-10) REVERT: A 51 ILE cc_start: 0.8447 (mt) cc_final: 0.8117 (mt) REVERT: A 53 ARG cc_start: 0.9682 (ptm-80) cc_final: 0.9413 (ptm160) REVERT: A 73 GLU cc_start: 0.8320 (tt0) cc_final: 0.7882 (tt0) REVERT: A 81 ASP cc_start: 0.8000 (t0) cc_final: 0.7791 (t0) REVERT: A 87 SER cc_start: 0.9044 (p) cc_final: 0.8592 (t) REVERT: A 89 VAL cc_start: 0.9031 (t) cc_final: 0.8733 (t) REVERT: A 90 MET cc_start: 0.8890 (mpp) cc_final: 0.8458 (mmm) REVERT: A 101 VAL cc_start: 0.9221 (t) cc_final: 0.9008 (t) REVERT: A 105 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8538 (tm-30) REVERT: A 126 LEU cc_start: 0.9536 (mm) cc_final: 0.9123 (mm) REVERT: A 130 ILE cc_start: 0.9547 (mm) cc_final: 0.9284 (mm) REVERT: B 25 ASN cc_start: 0.7982 (m110) cc_final: 0.7562 (m110) REVERT: B 39 ARG cc_start: 0.9313 (mmt-90) cc_final: 0.8650 (tpp-160) REVERT: B 49 LEU cc_start: 0.9538 (mm) cc_final: 0.9031 (tp) REVERT: B 64 ASN cc_start: 0.9006 (m-40) cc_final: 0.8755 (t0) REVERT: B 78 ARG cc_start: 0.9153 (mtm110) cc_final: 0.8569 (mtm110) REVERT: B 84 MET cc_start: 0.9404 (mpp) cc_final: 0.9102 (mpp) REVERT: B 87 VAL cc_start: 0.9812 (t) cc_final: 0.9604 (p) REVERT: B 91 LYS cc_start: 0.9704 (ttpt) cc_final: 0.9253 (ptmm) REVERT: C 50 TYR cc_start: 0.8599 (t80) cc_final: 0.7947 (t80) REVERT: C 90 ASP cc_start: 0.8629 (t0) cc_final: 0.8280 (t0) REVERT: C 94 ASN cc_start: 0.9480 (t0) cc_final: 0.9252 (m-40) REVERT: D 62 MET cc_start: 0.9163 (mmm) cc_final: 0.8956 (mmm) REVERT: D 85 LYS cc_start: 0.9433 (mtpt) cc_final: 0.9145 (mmmt) REVERT: D 101 LEU cc_start: 0.9163 (tt) cc_final: 0.8944 (tt) REVERT: E 50 GLU cc_start: 0.9219 (tp30) cc_final: 0.8880 (tp30) REVERT: E 60 LEU cc_start: 0.9284 (mt) cc_final: 0.8661 (mm) REVERT: E 74 ILE cc_start: 0.9426 (mt) cc_final: 0.9110 (mt) REVERT: E 77 ASP cc_start: 0.9626 (m-30) cc_final: 0.9405 (m-30) REVERT: E 120 MET cc_start: 0.9016 (mmm) cc_final: 0.8618 (mmm) REVERT: E 126 LEU cc_start: 0.9115 (tp) cc_final: 0.8913 (tp) REVERT: F 64 ASN cc_start: 0.8914 (m-40) cc_final: 0.8435 (m110) REVERT: F 87 VAL cc_start: 0.9789 (t) cc_final: 0.9472 (t) REVERT: F 91 LYS cc_start: 0.9478 (ttpt) cc_final: 0.9249 (ptpt) REVERT: H 34 LYS cc_start: 0.9243 (mmmt) cc_final: 0.9008 (mmmm) REVERT: H 47 GLN cc_start: 0.9215 (tm-30) cc_final: 0.8948 (tm-30) REVERT: H 49 HIS cc_start: 0.9024 (m-70) cc_final: 0.8589 (m90) REVERT: H 59 MET cc_start: 0.8992 (tpp) cc_final: 0.8709 (tpp) REVERT: H 68 ASP cc_start: 0.8909 (t0) cc_final: 0.8588 (t0) REVERT: H 69 ILE cc_start: 0.9138 (mm) cc_final: 0.8674 (mm) REVERT: H 76 GLU cc_start: 0.9316 (mm-30) cc_final: 0.9112 (mm-30) REVERT: H 105 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8751 (mm-30) REVERT: H 109 HIS cc_start: 0.8944 (m-70) cc_final: 0.8286 (m90) REVERT: H 113 GLU cc_start: 0.9439 (mm-30) cc_final: 0.8988 (mm-30) outliers start: 1 outliers final: 0 residues processed: 340 average time/residue: 0.1467 time to fit residues: 70.2855 Evaluate side-chains 271 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 270 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 52 optimal weight: 40.0000 chunk 30 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 ** P 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN ** 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 63 ASN H 82 HIS ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.071719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.051450 restraints weight = 88079.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.052619 restraints weight = 46241.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.053411 restraints weight = 30776.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.053861 restraints weight = 24183.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.054095 restraints weight = 21041.162| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 15895 Z= 0.323 Angle : 0.742 8.124 22928 Z= 0.433 Chirality : 0.042 0.208 2563 Planarity : 0.006 0.093 1719 Dihedral : 30.574 160.975 4918 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.80 % Favored : 96.89 % Rotamer: Outliers : 0.60 % Allowed : 4.31 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.27), residues: 964 helix: 1.73 (0.20), residues: 628 sheet: -1.83 (0.98), residues: 24 loop : -0.56 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 92 TYR 0.028 0.002 TYR F 88 PHE 0.013 0.002 PHE F 61 TRP 0.018 0.003 TRP O 214 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00700 (15895) covalent geometry : angle 0.74154 (22928) hydrogen bonds : bond 0.06922 ( 895) hydrogen bonds : angle 3.92289 ( 2235) *********************** 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 306 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 301 time to evaluate : 0.424 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: O 183 ILE cc_start: 0.5398 (mt) cc_final: 0.5172 (mt) REVERT: P 181 MET cc_start: 0.4642 (tpt) cc_final: 0.3941 (mmt) REVERT: G 64 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.8880 (pp20) REVERT: G 68 ASN cc_start: 0.9587 (m-40) cc_final: 0.8932 (m110) REVERT: G 87 ILE cc_start: 0.9556 (mt) cc_final: 0.8923 (tp) REVERT: G 94 ASN cc_start: 0.9248 (t0) cc_final: 0.8994 (m-40) REVERT: A 51 ILE cc_start: 0.8749 (mt) cc_final: 0.8360 (mt) REVERT: A 61 LEU cc_start: 0.8387 (mt) cc_final: 0.8089 (mt) REVERT: A 73 GLU cc_start: 0.8201 (tt0) cc_final: 0.7856 (tt0) REVERT: A 87 SER cc_start: 0.9176 (p) cc_final: 0.8564 (t) REVERT: A 90 MET cc_start: 0.8941 (mpp) cc_final: 0.8628 (mpp) REVERT: A 105 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8400 (tm-30) REVERT: B 25 ASN cc_start: 0.8137 (m110) cc_final: 0.7829 (m110) REVERT: B 39 ARG cc_start: 0.9115 (mmt-90) cc_final: 0.8548 (tpp-160) REVERT: B 43 VAL cc_start: 0.9155 (t) cc_final: 0.8831 (p) REVERT: B 49 LEU cc_start: 0.9467 (mm) cc_final: 0.8948 (tp) REVERT: B 68 ASP cc_start: 0.8873 (m-30) cc_final: 0.8607 (m-30) REVERT: B 84 MET cc_start: 0.9387 (mpp) cc_final: 0.9125 (mpp) REVERT: B 91 LYS cc_start: 0.9631 (ttpt) cc_final: 0.9340 (ptmm) REVERT: C 50 TYR cc_start: 0.8953 (t80) cc_final: 0.8399 (t80) REVERT: C 74 LYS cc_start: 0.9369 (mmtm) cc_final: 0.9148 (mmtm) REVERT: C 87 ILE cc_start: 0.9408 (mt) cc_final: 0.9202 (mt) REVERT: C 90 ASP cc_start: 0.8766 (t0) cc_final: 0.8353 (t0) REVERT: C 94 ASN cc_start: 0.9484 (t0) cc_final: 0.9193 (m-40) REVERT: D 62 MET cc_start: 0.9316 (mmm) cc_final: 0.8909 (mmm) REVERT: D 102 LEU cc_start: 0.8623 (mp) cc_final: 0.8332 (mp) REVERT: D 105 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8847 (mm-30) REVERT: E 50 GLU cc_start: 0.9082 (tp30) cc_final: 0.8440 (tp30) REVERT: E 60 LEU cc_start: 0.9235 (mt) cc_final: 0.9016 (mm) REVERT: E 77 ASP cc_start: 0.9594 (m-30) cc_final: 0.9340 (m-30) REVERT: E 93 GLN cc_start: 0.9014 (tt0) cc_final: 0.8753 (tt0) REVERT: E 106 ASP cc_start: 0.8981 (m-30) cc_final: 0.8767 (m-30) REVERT: E 119 ILE cc_start: 0.9471 (pt) cc_final: 0.9201 (pt) REVERT: E 120 MET cc_start: 0.8870 (mmm) cc_final: 0.8534 (mmm) REVERT: F 25 ASN cc_start: 0.8535 (m-40) cc_final: 0.8017 (m-40) REVERT: F 63 GLU cc_start: 0.9370 (pt0) cc_final: 0.8800 (pp20) REVERT: F 84 MET cc_start: 0.9322 (tpt) cc_final: 0.8791 (tpp) REVERT: F 91 LYS cc_start: 0.9456 (ttpt) cc_final: 0.9081 (mtmt) REVERT: H 34 LYS cc_start: 0.9209 (mmmt) cc_final: 0.9006 (mmmm) REVERT: H 47 GLN cc_start: 0.9284 (tm-30) cc_final: 0.9063 (tm-30) REVERT: H 49 HIS cc_start: 0.8941 (m-70) cc_final: 0.8527 (m-70) REVERT: H 59 MET cc_start: 0.9035 (tpp) cc_final: 0.8561 (tpp) REVERT: H 63 ASN cc_start: 0.9279 (m-40) cc_final: 0.8927 (m110) REVERT: H 82 HIS cc_start: 0.8912 (OUTLIER) cc_final: 0.8433 (m90) REVERT: H 109 HIS cc_start: 0.8963 (m-70) cc_final: 0.8190 (m90) REVERT: H 113 GLU cc_start: 0.9373 (mm-30) cc_final: 0.8766 (mm-30) outliers start: 5 outliers final: 1 residues processed: 303 average time/residue: 0.1455 time to fit residues: 62.4151 Evaluate side-chains 250 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 247 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 97 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 43 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.075852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.055712 restraints weight = 84753.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.056852 restraints weight = 44937.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.057593 restraints weight = 30118.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.058083 restraints weight = 23915.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.058389 restraints weight = 20560.099| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15895 Z= 0.173 Angle : 0.637 8.168 22928 Z= 0.378 Chirality : 0.037 0.214 2563 Planarity : 0.005 0.093 1719 Dihedral : 30.483 157.662 4918 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.39 % Favored : 97.41 % Rotamer: Outliers : 0.12 % Allowed : 1.92 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.27), residues: 964 helix: 1.91 (0.20), residues: 628 sheet: -1.97 (0.93), residues: 24 loop : -0.47 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 77 TYR 0.020 0.002 TYR F 88 PHE 0.022 0.002 PHE D 70 TRP 0.014 0.002 TRP P 214 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00372 (15895) covalent geometry : angle 0.63746 (22928) hydrogen bonds : bond 0.04037 ( 895) hydrogen bonds : angle 3.38126 ( 2235) *********************** 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 325 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 324 time to evaluate : 0.412 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: O 215 GLN cc_start: 0.9420 (pt0) cc_final: 0.9144 (pt0) REVERT: P 181 MET cc_start: 0.4202 (tpt) cc_final: 0.3617 (mmp) REVERT: G 25 PHE cc_start: 0.8207 (m-10) cc_final: 0.7968 (m-10) REVERT: G 62 ILE cc_start: 0.9656 (mt) cc_final: 0.9312 (mt) REVERT: G 84 GLN cc_start: 0.8933 (tp40) cc_final: 0.8578 (tp-100) REVERT: G 87 ILE cc_start: 0.9549 (mt) cc_final: 0.8968 (tp) REVERT: G 94 ASN cc_start: 0.9233 (t0) cc_final: 0.9021 (m-40) REVERT: A 51 ILE cc_start: 0.8411 (mt) cc_final: 0.8146 (mt) REVERT: A 54 TYR cc_start: 0.9525 (m-80) cc_final: 0.8836 (m-80) REVERT: A 87 SER cc_start: 0.9115 (p) cc_final: 0.8714 (t) REVERT: A 90 MET cc_start: 0.8681 (mpp) cc_final: 0.8379 (mmm) REVERT: A 105 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8434 (tm-30) REVERT: A 120 MET cc_start: 0.8585 (mmt) cc_final: 0.8283 (mmm) REVERT: B 39 ARG cc_start: 0.9100 (mmt-90) cc_final: 0.8606 (tpp-160) REVERT: B 43 VAL cc_start: 0.9042 (t) cc_final: 0.8698 (p) REVERT: B 84 MET cc_start: 0.9240 (mpp) cc_final: 0.8996 (mpp) REVERT: B 87 VAL cc_start: 0.9740 (t) cc_final: 0.9444 (p) REVERT: B 91 LYS cc_start: 0.9609 (ttpt) cc_final: 0.9067 (mmtp) REVERT: C 39 TYR cc_start: 0.8898 (m-80) cc_final: 0.8091 (m-80) REVERT: C 74 LYS cc_start: 0.9339 (mmtm) cc_final: 0.9103 (mppt) REVERT: C 75 LYS cc_start: 0.9007 (tptm) cc_final: 0.8527 (tptp) REVERT: C 90 ASP cc_start: 0.8574 (t0) cc_final: 0.8209 (t0) REVERT: D 34 LYS cc_start: 0.8693 (pptt) cc_final: 0.8428 (mmtp) REVERT: D 44 VAL cc_start: 0.9639 (p) cc_final: 0.9310 (p) REVERT: D 68 ASP cc_start: 0.9324 (t0) cc_final: 0.9051 (t0) REVERT: D 76 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8785 (mm-30) REVERT: E 48 LEU cc_start: 0.9375 (mt) cc_final: 0.9161 (mt) REVERT: E 50 GLU cc_start: 0.9065 (tp30) cc_final: 0.8692 (tp30) REVERT: E 60 LEU cc_start: 0.9125 (mt) cc_final: 0.8857 (mm) REVERT: E 73 GLU cc_start: 0.9315 (pt0) cc_final: 0.8518 (pt0) REVERT: E 74 ILE cc_start: 0.9468 (mt) cc_final: 0.9168 (mt) REVERT: E 77 ASP cc_start: 0.9508 (m-30) cc_final: 0.9199 (m-30) REVERT: E 93 GLN cc_start: 0.8865 (tt0) cc_final: 0.8541 (tt0) REVERT: E 99 TYR cc_start: 0.8955 (t80) cc_final: 0.8725 (t80) REVERT: E 119 ILE cc_start: 0.9435 (pt) cc_final: 0.9201 (pt) REVERT: E 120 MET cc_start: 0.9094 (mmm) cc_final: 0.8432 (mmm) REVERT: F 25 ASN cc_start: 0.9158 (m-40) cc_final: 0.8310 (m-40) REVERT: F 44 LYS cc_start: 0.8854 (tptm) cc_final: 0.8576 (tppt) REVERT: F 63 GLU cc_start: 0.9324 (pt0) cc_final: 0.8952 (pp20) REVERT: F 84 MET cc_start: 0.8944 (tpt) cc_final: 0.8719 (tpp) REVERT: H 40 TYR cc_start: 0.8505 (m-80) cc_final: 0.8280 (m-80) REVERT: H 49 HIS cc_start: 0.8833 (m-70) cc_final: 0.8619 (m-70) REVERT: H 69 ILE cc_start: 0.9017 (mm) cc_final: 0.8601 (mm) REVERT: H 109 HIS cc_start: 0.9052 (m-70) cc_final: 0.7922 (m-70) REVERT: H 113 GLU cc_start: 0.9305 (mm-30) cc_final: 0.8640 (mm-30) outliers start: 1 outliers final: 0 residues processed: 324 average time/residue: 0.1481 time to fit residues: 67.6769 Evaluate side-chains 260 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 85 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 65 optimal weight: 0.0060 chunk 6 optimal weight: 0.0030 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 overall best weight: 0.5606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 68 ASN A 93 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.077732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.057295 restraints weight = 83252.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.058584 restraints weight = 44111.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.059377 restraints weight = 29496.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.059944 restraints weight = 23269.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.060304 restraints weight = 19869.231| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4682 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= 0.157 Angle : 0.628 8.475 22928 Z= 0.371 Chirality : 0.036 0.167 2563 Planarity : 0.005 0.094 1719 Dihedral : 30.250 151.222 4918 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.70 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.27), residues: 964 helix: 1.76 (0.20), residues: 628 sheet: -1.83 (0.94), residues: 24 loop : -0.59 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 33 TYR 0.022 0.002 TYR C 50 PHE 0.012 0.001 PHE E 67 TRP 0.013 0.002 TRP O 214 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00329 (15895) covalent geometry : angle 0.62783 (22928) hydrogen bonds : bond 0.03700 ( 895) hydrogen bonds : angle 3.20952 ( 2235) *********************** 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 325 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.377 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: P 181 MET cc_start: 0.4292 (tpt) cc_final: 0.3767 (mmp) REVERT: G 62 ILE cc_start: 0.9637 (mt) cc_final: 0.9251 (mt) REVERT: G 68 ASN cc_start: 0.9571 (m-40) cc_final: 0.9305 (m-40) REVERT: G 87 ILE cc_start: 0.9570 (mt) cc_final: 0.9031 (tp) REVERT: G 92 GLU cc_start: 0.6704 (tt0) cc_final: 0.6375 (tp30) REVERT: G 94 ASN cc_start: 0.9210 (t0) cc_final: 0.9004 (m-40) REVERT: A 50 GLU cc_start: 0.9451 (mt-10) cc_final: 0.8992 (mt-10) REVERT: A 54 TYR cc_start: 0.9451 (m-80) cc_final: 0.9056 (m-80) REVERT: A 87 SER cc_start: 0.8842 (p) cc_final: 0.8460 (t) REVERT: A 90 MET cc_start: 0.8962 (mpp) cc_final: 0.8557 (mmm) REVERT: A 105 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8396 (tm-30) REVERT: A 120 MET cc_start: 0.8597 (mmt) cc_final: 0.8334 (mmt) REVERT: A 130 ILE cc_start: 0.9351 (mm) cc_final: 0.9092 (mm) REVERT: B 84 MET cc_start: 0.9284 (mpp) cc_final: 0.8937 (mpp) REVERT: B 91 LYS cc_start: 0.9609 (ttpt) cc_final: 0.9076 (mmtp) REVERT: C 39 TYR cc_start: 0.8731 (m-80) cc_final: 0.8244 (m-80) REVERT: C 74 LYS cc_start: 0.9313 (mmtm) cc_final: 0.9096 (mppt) REVERT: C 84 GLN cc_start: 0.9099 (tp-100) cc_final: 0.8882 (tp-100) REVERT: C 90 ASP cc_start: 0.8133 (t0) cc_final: 0.7718 (t0) REVERT: D 34 LYS cc_start: 0.8811 (pptt) cc_final: 0.8521 (mmtp) REVERT: D 44 VAL cc_start: 0.9634 (p) cc_final: 0.9275 (p) REVERT: D 51 ASP cc_start: 0.8620 (p0) cc_final: 0.8411 (m-30) REVERT: D 76 GLU cc_start: 0.9290 (mm-30) cc_final: 0.8797 (mm-30) REVERT: D 83 TYR cc_start: 0.8312 (m-10) cc_final: 0.7588 (m-10) REVERT: D 85 LYS cc_start: 0.9438 (mtpt) cc_final: 0.8997 (mmmt) REVERT: E 48 LEU cc_start: 0.9323 (mt) cc_final: 0.9021 (mt) REVERT: E 50 GLU cc_start: 0.9104 (tp30) cc_final: 0.8717 (tp30) REVERT: E 60 LEU cc_start: 0.9276 (mt) cc_final: 0.9054 (mm) REVERT: E 73 GLU cc_start: 0.9305 (pt0) cc_final: 0.8410 (pt0) REVERT: E 74 ILE cc_start: 0.9463 (mt) cc_final: 0.9175 (mt) REVERT: E 77 ASP cc_start: 0.9488 (m-30) cc_final: 0.9262 (m-30) REVERT: E 93 GLN cc_start: 0.8899 (tt0) cc_final: 0.8623 (tt0) REVERT: E 105 GLU cc_start: 0.8796 (pp20) cc_final: 0.8524 (pp20) REVERT: E 106 ASP cc_start: 0.9091 (m-30) cc_final: 0.8781 (m-30) REVERT: E 120 MET cc_start: 0.8939 (mmm) cc_final: 0.8460 (mmm) REVERT: F 25 ASN cc_start: 0.9297 (m-40) cc_final: 0.8746 (m110) REVERT: F 49 LEU cc_start: 0.9465 (mt) cc_final: 0.9221 (mm) REVERT: F 63 GLU cc_start: 0.9297 (pt0) cc_final: 0.8900 (pp20) REVERT: F 100 PHE cc_start: 0.8354 (m-10) cc_final: 0.8138 (m-10) REVERT: H 59 MET cc_start: 0.8772 (tpp) cc_final: 0.8540 (tpp) REVERT: H 69 ILE cc_start: 0.8941 (mm) cc_final: 0.8582 (mm) REVERT: H 108 LYS cc_start: 0.9441 (ptmm) cc_final: 0.9192 (pttm) REVERT: H 109 HIS cc_start: 0.8899 (m-70) cc_final: 0.8115 (m-70) REVERT: H 113 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8589 (mm-30) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.1473 time to fit residues: 67.5264 Evaluate side-chains 257 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 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 = 0.3587 r_free = 0.3587 target = 0.073479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.053364 restraints weight = 86912.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.054443 restraints weight = 46857.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.055245 restraints weight = 32042.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.055754 restraints weight = 25488.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.056081 restraints weight = 21921.610| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15895 Z= 0.240 Angle : 0.679 9.145 22928 Z= 0.401 Chirality : 0.038 0.252 2563 Planarity : 0.006 0.095 1719 Dihedral : 30.467 154.296 4918 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.32 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.27), residues: 964 helix: 1.58 (0.20), residues: 626 sheet: -2.06 (0.93), residues: 24 loop : -0.69 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 33 TYR 0.028 0.002 TYR B 88 PHE 0.026 0.002 PHE A 67 TRP 0.018 0.003 TRP O 214 HIS 0.008 0.002 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00523 (15895) covalent geometry : angle 0.67883 (22928) hydrogen bonds : bond 0.05713 ( 895) hydrogen bonds : angle 3.56474 ( 2235) *********************** 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 293 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.451 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: 0.4340 (tpt) cc_final: 0.3727 (mmt) REVERT: G 68 ASN cc_start: 0.9476 (m-40) cc_final: 0.9182 (p0) REVERT: G 88 ARG cc_start: 0.8660 (mmt180) cc_final: 0.7768 (mtp180) REVERT: A 87 SER cc_start: 0.9040 (p) cc_final: 0.8549 (t) REVERT: A 90 MET cc_start: 0.9005 (mpp) cc_final: 0.8705 (mmm) REVERT: A 105 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8412 (tm-30) REVERT: A 120 MET cc_start: 0.8540 (mmt) cc_final: 0.8255 (mmm) REVERT: B 49 LEU cc_start: 0.9295 (mm) cc_final: 0.8865 (tp) REVERT: B 63 GLU cc_start: 0.8605 (pp20) cc_final: 0.8365 (pp20) REVERT: B 84 MET cc_start: 0.9250 (mpp) cc_final: 0.9023 (mpp) REVERT: B 91 LYS cc_start: 0.9606 (ttpt) cc_final: 0.9194 (mmtp) REVERT: C 74 LYS cc_start: 0.9279 (mmtm) cc_final: 0.9036 (mppt) REVERT: C 79 ILE cc_start: 0.9134 (tt) cc_final: 0.8811 (mm) REVERT: C 84 GLN cc_start: 0.9126 (tp-100) cc_final: 0.8843 (tp-100) REVERT: C 90 ASP cc_start: 0.8455 (t0) cc_final: 0.8088 (t0) REVERT: D 34 LYS cc_start: 0.8899 (pptt) cc_final: 0.8353 (mmtp) REVERT: D 76 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8606 (mm-30) REVERT: E 50 GLU cc_start: 0.9067 (tp30) cc_final: 0.8618 (tp30) REVERT: E 60 LEU cc_start: 0.9234 (mt) cc_final: 0.9017 (mm) REVERT: E 74 ILE cc_start: 0.9489 (mt) cc_final: 0.9182 (mt) REVERT: E 77 ASP cc_start: 0.9495 (m-30) cc_final: 0.9237 (m-30) REVERT: E 106 ASP cc_start: 0.9006 (m-30) cc_final: 0.8511 (m-30) REVERT: E 119 ILE cc_start: 0.9468 (pt) cc_final: 0.9212 (pt) REVERT: E 120 MET cc_start: 0.9042 (mmm) cc_final: 0.8476 (mmm) REVERT: F 63 GLU cc_start: 0.9264 (pt0) cc_final: 0.8884 (pp20) REVERT: F 88 TYR cc_start: 0.8571 (m-10) cc_final: 0.7649 (m-10) REVERT: H 59 MET cc_start: 0.8763 (tpp) cc_final: 0.8517 (tpp) REVERT: H 69 ILE cc_start: 0.9035 (mm) cc_final: 0.8652 (mm) REVERT: H 108 LYS cc_start: 0.9388 (ptmm) cc_final: 0.9159 (pptt) REVERT: H 113 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8623 (mm-30) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.1376 time to fit residues: 57.9488 Evaluate side-chains 242 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 123 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 121 optimal weight: 0.0670 chunk 83 optimal weight: 9.9990 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 84 GLN ** A 93 GLN ** 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** D 109 HIS F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.074098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.053905 restraints weight = 87371.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.054972 restraints weight = 46806.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.055726 restraints weight = 31498.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.056240 restraints weight = 25208.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.056578 restraints weight = 21788.498| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15895 Z= 0.209 Angle : 0.665 8.403 22928 Z= 0.392 Chirality : 0.038 0.238 2563 Planarity : 0.005 0.096 1719 Dihedral : 30.499 151.867 4918 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.84 % Favored : 95.95 % Rotamer: Outliers : 0.12 % Allowed : 1.32 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.27), residues: 964 helix: 1.52 (0.20), residues: 624 sheet: -1.86 (0.94), residues: 24 loop : -0.57 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 213 TYR 0.020 0.002 TYR C 50 PHE 0.022 0.002 PHE A 67 TRP 0.010 0.002 TRP P 214 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00454 (15895) covalent geometry : angle 0.66477 (22928) hydrogen bonds : bond 0.04698 ( 895) hydrogen bonds : angle 3.50368 ( 2235) *********************** 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 292 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 291 time to evaluate : 0.454 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 183 ILE cc_start: 0.4919 (mt) cc_final: 0.4691 (mt) REVERT: O 201 MET cc_start: 0.7460 (mpp) cc_final: 0.7101 (mpp) REVERT: P 181 MET cc_start: 0.4648 (tpt) cc_final: 0.3960 (mmt) REVERT: G 56 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8643 (tm-30) REVERT: G 62 ILE cc_start: 0.9586 (mt) cc_final: 0.9212 (mt) REVERT: A 87 SER cc_start: 0.8960 (p) cc_final: 0.8531 (t) REVERT: A 90 MET cc_start: 0.8998 (mpp) cc_final: 0.8666 (mmm) REVERT: A 105 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8375 (tm-30) REVERT: A 126 LEU cc_start: 0.9490 (mm) cc_final: 0.9178 (mm) REVERT: A 130 ILE cc_start: 0.9359 (mm) cc_final: 0.9137 (mm) REVERT: B 31 LYS cc_start: 0.9515 (tmmt) cc_final: 0.9300 (tmtt) REVERT: B 49 LEU cc_start: 0.9250 (mm) cc_final: 0.8747 (tp) REVERT: B 63 GLU cc_start: 0.8690 (pp20) cc_final: 0.8395 (pp20) REVERT: B 84 MET cc_start: 0.9330 (mpp) cc_final: 0.9060 (mpp) REVERT: B 91 LYS cc_start: 0.9582 (ttpt) cc_final: 0.9098 (mmtp) REVERT: C 36 LYS cc_start: 0.9437 (mmtm) cc_final: 0.9042 (mtmt) REVERT: C 74 LYS cc_start: 0.9298 (mmtm) cc_final: 0.9084 (mppt) REVERT: C 84 GLN cc_start: 0.9120 (tp-100) cc_final: 0.8841 (tp-100) REVERT: C 90 ASP cc_start: 0.8444 (t0) cc_final: 0.8152 (t0) REVERT: D 34 LYS cc_start: 0.8960 (pptt) cc_final: 0.8411 (mmtp) REVERT: D 76 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8682 (mm-30) REVERT: D 85 LYS cc_start: 0.9469 (mtpt) cc_final: 0.9011 (mmmt) REVERT: D 109 HIS cc_start: 0.8826 (OUTLIER) cc_final: 0.8517 (m90) REVERT: E 50 GLU cc_start: 0.9031 (tp30) cc_final: 0.8593 (tp30) REVERT: E 60 LEU cc_start: 0.9158 (mt) cc_final: 0.8919 (mm) REVERT: E 74 ILE cc_start: 0.9465 (mt) cc_final: 0.9172 (mt) REVERT: E 77 ASP cc_start: 0.9454 (m-30) cc_final: 0.9224 (m-30) REVERT: E 93 GLN cc_start: 0.8949 (tt0) cc_final: 0.8678 (tt0) REVERT: E 119 ILE cc_start: 0.9494 (pt) cc_final: 0.9286 (pt) REVERT: E 120 MET cc_start: 0.9134 (mmm) cc_final: 0.8396 (mmm) REVERT: F 63 GLU cc_start: 0.9212 (pt0) cc_final: 0.8864 (pp20) REVERT: F 66 ILE cc_start: 0.9647 (mm) cc_final: 0.9312 (mt) REVERT: F 68 ASP cc_start: 0.9139 (m-30) cc_final: 0.8858 (m-30) REVERT: F 88 TYR cc_start: 0.8686 (m-10) cc_final: 0.8058 (m-80) REVERT: H 69 ILE cc_start: 0.9036 (mm) cc_final: 0.8646 (mm) REVERT: H 76 GLU cc_start: 0.9060 (mp0) cc_final: 0.8352 (mp0) REVERT: H 108 LYS cc_start: 0.9442 (ptmm) cc_final: 0.9149 (pptt) REVERT: H 113 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8575 (mm-30) REVERT: H 116 LYS cc_start: 0.9278 (pttm) cc_final: 0.9040 (pttm) outliers start: 1 outliers final: 0 residues processed: 291 average time/residue: 0.1399 time to fit residues: 58.7634 Evaluate side-chains 243 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 242 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 25 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** 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** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 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 = 0.3565 r_free = 0.3565 target = 0.072374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.051736 restraints weight = 91296.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.052710 restraints weight = 50860.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.053408 restraints weight = 34993.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.053869 restraints weight = 28182.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.054113 restraints weight = 24687.766| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15895 Z= 0.248 Angle : 0.701 8.387 22928 Z= 0.412 Chirality : 0.039 0.249 2563 Planarity : 0.006 0.096 1719 Dihedral : 30.641 153.773 4918 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.15 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.27), residues: 964 helix: 1.37 (0.20), residues: 625 sheet: -1.93 (0.96), residues: 24 loop : -0.64 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 213 TYR 0.038 0.002 TYR B 88 PHE 0.027 0.002 PHE A 67 TRP 0.015 0.002 TRP P 244 HIS 0.009 0.002 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00539 (15895) covalent geometry : angle 0.70056 (22928) hydrogen bonds : bond 0.05762 ( 895) hydrogen bonds : angle 3.73731 ( 2235) *********************** 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 280 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.557 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: G 39 TYR cc_start: 0.8891 (m-80) cc_final: 0.8481 (m-80) REVERT: G 68 ASN cc_start: 0.9520 (m-40) cc_final: 0.9273 (m110) REVERT: A 87 SER cc_start: 0.9079 (p) cc_final: 0.8576 (t) REVERT: A 90 MET cc_start: 0.9020 (mpp) cc_final: 0.8653 (mmm) REVERT: A 105 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8386 (tm-30) REVERT: A 120 MET cc_start: 0.8721 (mmt) cc_final: 0.8491 (mmt) REVERT: B 49 LEU cc_start: 0.9255 (mm) cc_final: 0.8726 (tp) REVERT: B 63 GLU cc_start: 0.8707 (pp20) cc_final: 0.8500 (pp20) REVERT: B 91 LYS cc_start: 0.9581 (ttpt) cc_final: 0.9151 (mmtt) REVERT: C 74 LYS cc_start: 0.9281 (mmtm) cc_final: 0.9070 (mppt) REVERT: C 84 GLN cc_start: 0.9044 (tp-100) cc_final: 0.8769 (tp-100) REVERT: C 90 ASP cc_start: 0.8495 (t0) cc_final: 0.8201 (t0) REVERT: D 34 LYS cc_start: 0.9045 (pptt) cc_final: 0.8481 (mmtp) REVERT: D 76 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8688 (mm-30) REVERT: D 85 LYS cc_start: 0.9469 (mtpt) cc_final: 0.9002 (mmmt) REVERT: D 102 LEU cc_start: 0.7943 (mp) cc_final: 0.7699 (mp) REVERT: E 50 GLU cc_start: 0.8954 (tp30) cc_final: 0.8530 (tp30) REVERT: E 60 LEU cc_start: 0.9152 (mt) cc_final: 0.8906 (mm) REVERT: E 74 ILE cc_start: 0.9418 (mt) cc_final: 0.9125 (mt) REVERT: E 77 ASP cc_start: 0.9396 (m-30) cc_final: 0.9172 (m-30) REVERT: E 106 ASP cc_start: 0.9006 (m-30) cc_final: 0.8584 (m-30) REVERT: E 119 ILE cc_start: 0.9483 (pt) cc_final: 0.9247 (pt) REVERT: E 120 MET cc_start: 0.9072 (mmm) cc_final: 0.8513 (mmm) REVERT: F 63 GLU cc_start: 0.9197 (pt0) cc_final: 0.8819 (pp20) REVERT: F 64 ASN cc_start: 0.9567 (t0) cc_final: 0.9207 (t0) REVERT: F 68 ASP cc_start: 0.9181 (m-30) cc_final: 0.8918 (m-30) REVERT: F 88 TYR cc_start: 0.8674 (m-10) cc_final: 0.8183 (m-80) REVERT: H 59 MET cc_start: 0.8855 (tpp) cc_final: 0.8529 (tpp) REVERT: H 69 ILE cc_start: 0.9051 (mm) cc_final: 0.8647 (mm) REVERT: H 108 LYS cc_start: 0.9451 (ptmm) cc_final: 0.9160 (pptt) REVERT: H 113 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8509 (mm-30) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.1426 time to fit residues: 57.3027 Evaluate side-chains 227 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 99 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 48 optimal weight: 0.0980 chunk 70 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 220 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** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.075747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.055504 restraints weight = 85438.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.056614 restraints weight = 46882.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.057398 restraints weight = 32077.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.057926 restraints weight = 25608.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.058212 restraints weight = 22004.644| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.5870 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= 0.166 Angle : 0.666 8.408 22928 Z= 0.390 Chirality : 0.037 0.212 2563 Planarity : 0.005 0.095 1719 Dihedral : 30.444 151.279 4918 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.84 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.27), residues: 964 helix: 1.37 (0.20), residues: 626 sheet: -1.70 (1.00), residues: 24 loop : -0.65 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 219 TYR 0.020 0.002 TYR C 57 PHE 0.024 0.001 PHE A 67 TRP 0.014 0.002 TRP O 214 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00356 (15895) covalent geometry : angle 0.66641 (22928) hydrogen bonds : bond 0.03955 ( 895) hydrogen bonds : angle 3.49410 ( 2235) *********************** 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 290 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.337 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: O 183 ILE cc_start: 0.4900 (mt) cc_final: 0.4687 (mt) REVERT: P 181 MET cc_start: 0.4485 (tpt) cc_final: 0.3771 (mmt) REVERT: G 39 TYR cc_start: 0.8826 (m-80) cc_final: 0.8469 (m-80) REVERT: G 62 ILE cc_start: 0.9674 (mt) cc_final: 0.9325 (mt) REVERT: G 68 ASN cc_start: 0.9493 (m-40) cc_final: 0.9173 (m110) REVERT: A 87 SER cc_start: 0.8847 (p) cc_final: 0.8369 (t) REVERT: A 89 VAL cc_start: 0.8938 (m) cc_final: 0.8595 (m) REVERT: A 90 MET cc_start: 0.9029 (mpp) cc_final: 0.8725 (mmm) REVERT: A 94 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8220 (mt-10) REVERT: A 105 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8360 (tm-30) REVERT: A 120 MET cc_start: 0.8616 (mmt) cc_final: 0.8348 (mmt) REVERT: B 31 LYS cc_start: 0.9461 (tmtt) cc_final: 0.9209 (tmtt) REVERT: B 49 LEU cc_start: 0.9299 (mm) cc_final: 0.8803 (tp) REVERT: B 63 GLU cc_start: 0.8685 (pp20) cc_final: 0.8425 (pp20) REVERT: B 84 MET cc_start: 0.9264 (mpp) cc_final: 0.9048 (mpp) REVERT: C 36 LYS cc_start: 0.9402 (mmtm) cc_final: 0.9058 (mtmt) REVERT: C 84 GLN cc_start: 0.9070 (tp-100) cc_final: 0.8806 (tp-100) REVERT: C 90 ASP cc_start: 0.8075 (t0) cc_final: 0.7869 (t0) REVERT: D 34 LYS cc_start: 0.8848 (pptt) cc_final: 0.8367 (mmtp) REVERT: D 76 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8660 (mm-30) REVERT: D 83 TYR cc_start: 0.8389 (m-10) cc_final: 0.7909 (m-10) REVERT: D 85 LYS cc_start: 0.9467 (mtpt) cc_final: 0.9004 (mmmt) REVERT: D 96 THR cc_start: 0.9427 (m) cc_final: 0.9104 (p) REVERT: E 50 GLU cc_start: 0.9028 (tp30) cc_final: 0.8596 (tp30) REVERT: E 77 ASP cc_start: 0.9373 (m-30) cc_final: 0.9123 (m-30) REVERT: E 93 GLN cc_start: 0.8699 (tt0) cc_final: 0.8445 (tt0) REVERT: E 106 ASP cc_start: 0.9000 (m-30) cc_final: 0.8595 (m-30) REVERT: E 120 MET cc_start: 0.9009 (mmm) cc_final: 0.8334 (mmm) REVERT: F 49 LEU cc_start: 0.9447 (mt) cc_final: 0.9101 (mt) REVERT: F 63 GLU cc_start: 0.9232 (pt0) cc_final: 0.8809 (pp20) REVERT: F 64 ASN cc_start: 0.9572 (t0) cc_final: 0.9234 (t0) REVERT: F 66 ILE cc_start: 0.9633 (mm) cc_final: 0.9270 (mt) REVERT: F 68 ASP cc_start: 0.9027 (m-30) cc_final: 0.8713 (m-30) REVERT: F 88 TYR cc_start: 0.8703 (m-10) cc_final: 0.8016 (m-80) REVERT: H 59 MET cc_start: 0.8609 (tpp) cc_final: 0.8331 (tpp) REVERT: H 69 ILE cc_start: 0.9028 (mm) cc_final: 0.8656 (mm) REVERT: H 109 HIS cc_start: 0.8651 (m90) cc_final: 0.7942 (m90) REVERT: H 113 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8466 (mm-30) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.1423 time to fit residues: 59.4709 Evaluate side-chains 235 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 96 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 92 optimal weight: 0.0670 chunk 118 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 overall best weight: 1.3520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 220 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** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** H 82 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 = 0.3625 r_free = 0.3625 target = 0.075137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.054357 restraints weight = 88267.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.055470 restraints weight = 49091.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.056161 restraints weight = 34050.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.056742 restraints weight = 27327.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.057047 restraints weight = 23770.229| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.5994 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= 0.178 Angle : 0.675 8.118 22928 Z= 0.394 Chirality : 0.037 0.228 2563 Planarity : 0.005 0.096 1719 Dihedral : 30.392 151.205 4918 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.56 % Favored : 95.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.27), residues: 964 helix: 1.33 (0.20), residues: 626 sheet: -1.62 (1.04), residues: 24 loop : -0.67 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O 213 TYR 0.020 0.002 TYR C 57 PHE 0.026 0.002 PHE A 67 TRP 0.013 0.002 TRP O 214 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00385 (15895) covalent geometry : angle 0.67549 (22928) hydrogen bonds : bond 0.04225 ( 895) hydrogen bonds : angle 3.52373 ( 2235) ********************** 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 277 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7716 (mpp) cc_final: 0.7193 (mpp) REVERT: P 181 MET cc_start: 0.4513 (tpt) cc_final: 0.3804 (mmt) REVERT: G 68 ASN cc_start: 0.9448 (m-40) cc_final: 0.9150 (m110) REVERT: A 87 SER cc_start: 0.8881 (p) cc_final: 0.8445 (t) REVERT: A 94 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8137 (mt-10) REVERT: A 97 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8909 (mt-10) REVERT: B 31 LYS cc_start: 0.9452 (tmtt) cc_final: 0.9161 (tmtt) REVERT: B 49 LEU cc_start: 0.9260 (mm) cc_final: 0.8778 (tp) REVERT: B 84 MET cc_start: 0.9030 (mpp) cc_final: 0.8575 (mmm) REVERT: C 36 LYS cc_start: 0.9415 (mmtm) cc_final: 0.9045 (mtmt) REVERT: C 90 ASP cc_start: 0.8402 (t0) cc_final: 0.8067 (t0) REVERT: D 62 MET cc_start: 0.8827 (mmm) cc_final: 0.8619 (mmm) REVERT: D 76 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8626 (mm-30) REVERT: D 85 LYS cc_start: 0.9442 (mtpt) cc_final: 0.8985 (mmmt) REVERT: D 96 THR cc_start: 0.9419 (m) cc_final: 0.9180 (p) REVERT: E 50 GLU cc_start: 0.8983 (tp30) cc_final: 0.8559 (tp30) REVERT: E 77 ASP cc_start: 0.9327 (m-30) cc_final: 0.9084 (m-30) REVERT: E 93 GLN cc_start: 0.8771 (tt0) cc_final: 0.8354 (tt0) REVERT: E 106 ASP cc_start: 0.8919 (m-30) cc_final: 0.8482 (m-30) REVERT: E 120 MET cc_start: 0.9034 (mmm) cc_final: 0.8431 (mmm) REVERT: F 49 LEU cc_start: 0.9444 (mt) cc_final: 0.9102 (mt) REVERT: F 63 GLU cc_start: 0.9232 (pt0) cc_final: 0.8786 (pp20) REVERT: F 64 ASN cc_start: 0.9549 (t0) cc_final: 0.9214 (t0) REVERT: F 68 ASP cc_start: 0.9004 (m-30) cc_final: 0.8714 (m-30) REVERT: F 88 TYR cc_start: 0.8702 (m-10) cc_final: 0.8230 (m-80) REVERT: H 59 MET cc_start: 0.8671 (tpp) cc_final: 0.8334 (tpp) REVERT: H 69 ILE cc_start: 0.8986 (mm) cc_final: 0.8633 (mm) REVERT: H 95 GLN cc_start: 0.9445 (tt0) cc_final: 0.9150 (tt0) REVERT: H 109 HIS cc_start: 0.8610 (m90) cc_final: 0.8002 (m90) REVERT: H 113 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8416 (mm-30) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.1344 time to fit residues: 54.2151 Evaluate side-chains 238 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 55 optimal weight: 4.9990 chunk 74 optimal weight: 0.0030 chunk 80 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 220 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** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 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 = 0.3632 r_free = 0.3632 target = 0.075494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.055255 restraints weight = 86444.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.056419 restraints weight = 47726.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.057182 restraints weight = 32725.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.057725 restraints weight = 26118.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.058042 restraints weight = 22566.805| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.6163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15895 Z= 0.175 Angle : 0.674 8.653 22928 Z= 0.392 Chirality : 0.037 0.212 2563 Planarity : 0.005 0.096 1719 Dihedral : 30.367 150.794 4918 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 14.69 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.27), residues: 964 helix: 1.27 (0.20), residues: 626 sheet: -1.63 (1.00), residues: 24 loop : -0.74 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 213 TYR 0.023 0.002 TYR C 57 PHE 0.023 0.001 PHE A 67 TRP 0.014 0.002 TRP O 214 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00380 (15895) covalent geometry : angle 0.67373 (22928) hydrogen bonds : bond 0.04136 ( 895) hydrogen bonds : angle 3.50313 ( 2235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2936.74 seconds wall clock time: 51 minutes 28.32 seconds (3088.32 seconds total)