Starting phenix.real_space_refine on Fri Jun 13 04:06:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vfz_43195/06_2025/8vfz_43195.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vfz_43195/06_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_43195/06_2025/8vfz_43195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vfz_43195/06_2025/8vfz_43195.map" model { file = "/net/cci-nas-00/data/ceres_data/8vfz_43195/06_2025/8vfz_43195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vfz_43195/06_2025/8vfz_43195.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 342 5.49 5 S 28 5.16 5 C 8336 2.51 5 N 2764 2.21 5 O 3436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14906 Number of models: 1 Model: "" Number of chains: 12 Chain: "O" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 856 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain: "I" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3501 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "J" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3510 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "P" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 856 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain: "G" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 931 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Time building chain proxies: 8.13, per 1000 atoms: 0.55 Number of scatterers: 14906 At special positions: 0 Unit cell: (81.84, 137.28, 199.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 342 15.00 O 3436 8.00 N 2764 7.00 C 8336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.4 seconds 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 66.8% alpha, 2.8% beta 171 base pairs and 289 stacking pairs defined. Time for finding SS restraints: 6.21 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: 5.45 Time building geometry restraints manager: 3.91 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: 0.690 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.610 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.420 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.28), residues: 964 helix: 3.30 (0.21), residues: 622 sheet: -1.64 (0.94), residues: 24 loop : -0.35 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 214 HIS 0.002 0.001 HIS B 75 PHE 0.008 0.001 PHE P 224 TYR 0.007 0.001 TYR B 72 ARG 0.004 0.000 ARG O 265 Details of bonding type rmsd hydrogen bonds : bond 0.09641 ( 895) hydrogen bonds : angle 3.61872 ( 2235) covalent geometry : bond 0.00471 (15895) covalent geometry : angle 0.67647 (22928) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 450 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 204 PHE cc_start: 0.9280 (m-80) cc_final: 0.9021 (m-80) REVERT: O 260 LEU cc_start: 0.4439 (OUTLIER) cc_final: 0.3684 (tt) REVERT: P 175 TYR cc_start: 0.4490 (m-80) cc_final: 0.3490 (m-10) REVERT: G 23 LEU cc_start: 0.9433 (mt) cc_final: 0.9050 (mp) REVERT: G 24 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8075 (mm-40) REVERT: G 34 LEU cc_start: 0.9645 (mt) cc_final: 0.9432 (mt) REVERT: G 50 TYR cc_start: 0.8592 (t80) cc_final: 0.8381 (t80) REVERT: G 83 LEU cc_start: 0.9576 (mt) cc_final: 0.9330 (mt) REVERT: G 87 ILE cc_start: 0.9571 (mt) cc_final: 0.9297 (tp) REVERT: G 88 ARG cc_start: 0.8798 (mmt180) cc_final: 0.8191 (mtp180) REVERT: G 100 VAL cc_start: 0.9270 (t) cc_final: 0.8998 (p) REVERT: A 50 GLU cc_start: 0.9388 (mt-10) cc_final: 0.8780 (mt-10) REVERT: A 51 ILE cc_start: 0.8280 (mt) cc_final: 0.7983 (mt) REVERT: A 54 TYR cc_start: 0.9282 (m-80) cc_final: 0.8637 (m-80) REVERT: A 92 LEU cc_start: 0.8900 (mt) cc_final: 0.8688 (mt) REVERT: A 101 VAL cc_start: 0.9237 (t) cc_final: 0.8984 (t) REVERT: A 105 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8503 (tm-30) REVERT: B 39 ARG cc_start: 0.9188 (mmt-90) cc_final: 0.8428 (tpp-160) REVERT: B 68 ASP cc_start: 0.8814 (m-30) cc_final: 0.8492 (m-30) REVERT: B 70 VAL cc_start: 0.9680 (t) cc_final: 0.9344 (m) REVERT: B 87 VAL cc_start: 0.9811 (t) cc_final: 0.9589 (t) REVERT: B 91 LYS cc_start: 0.9690 (ttpt) cc_final: 0.9213 (ptmm) REVERT: C 38 ASN cc_start: 0.8671 (m110) cc_final: 0.8297 (t0) REVERT: C 50 TYR cc_start: 0.8243 (t80) cc_final: 0.7998 (t80) REVERT: C 51 LEU cc_start: 0.9684 (tp) cc_final: 0.9477 (tp) REVERT: C 90 ASP cc_start: 0.8882 (t0) cc_final: 0.8573 (t0) REVERT: C 92 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8750 (mt-10) REVERT: D 62 MET cc_start: 0.9190 (mmm) cc_final: 0.8915 (mmm) REVERT: D 85 LYS cc_start: 0.9370 (mtpt) cc_final: 0.9059 (mmmt) REVERT: D 87 SER cc_start: 0.9418 (m) cc_final: 0.8534 (p) REVERT: D 89 ILE cc_start: 0.9390 (mt) cc_final: 0.9185 (tp) REVERT: E 48 LEU cc_start: 0.9319 (mt) cc_final: 0.8954 (mt) REVERT: E 60 LEU cc_start: 0.9209 (mt) cc_final: 0.8000 (mp) REVERT: E 73 GLU cc_start: 0.8970 (tt0) cc_final: 0.8589 (mt-10) REVERT: E 93 GLN cc_start: 0.9059 (tt0) cc_final: 0.8246 (tm-30) REVERT: E 106 ASP cc_start: 0.9057 (m-30) cc_final: 0.8590 (m-30) REVERT: E 109 LEU cc_start: 0.9646 (mt) cc_final: 0.9210 (mm) REVERT: E 125 GLN cc_start: 0.9266 (mt0) cc_final: 0.8876 (mp10) REVERT: F 58 LEU cc_start: 0.9659 (tp) cc_final: 0.9415 (tp) REVERT: F 68 ASP cc_start: 0.8909 (m-30) cc_final: 0.8691 (m-30) REVERT: F 85 ASP cc_start: 0.9098 (m-30) cc_final: 0.8795 (t0) REVERT: F 87 VAL cc_start: 0.9752 (t) cc_final: 0.9449 (t) REVERT: F 91 LYS cc_start: 0.9430 (ttpt) cc_final: 0.9149 (ptpt) REVERT: H 38 SER cc_start: 0.9131 (m) cc_final: 0.8652 (p) REVERT: H 68 ASP cc_start: 0.8760 (t0) cc_final: 0.8478 (t0) REVERT: H 90 THR cc_start: 0.8750 (p) cc_final: 0.8214 (p) REVERT: H 91 SER cc_start: 0.9118 (p) cc_final: 0.8914 (t) REVERT: H 93 GLU cc_start: 0.8666 (mp0) cc_final: 0.8332 (mp0) REVERT: H 113 GLU cc_start: 0.9315 (mm-30) cc_final: 0.9006 (mm-30) outliers start: 10 outliers final: 2 residues processed: 456 average time/residue: 0.3245 time to fit residues: 202.4302 Evaluate side-chains 295 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 292 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 0.0170 chunk 116 optimal weight: 2.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 212 GLN ** O 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 215 GLN G 68 ASN G 89 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS B 93 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN H 63 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.078864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.057826 restraints weight = 82487.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.059188 restraints weight = 43366.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.060018 restraints weight = 28682.478| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15895 Z= 0.181 Angle : 0.638 7.908 22928 Z= 0.378 Chirality : 0.037 0.197 2563 Planarity : 0.006 0.092 1719 Dihedral : 29.984 160.382 4918 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.07 % Favored : 97.61 % Rotamer: Outliers : 0.24 % Allowed : 3.23 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.27), residues: 964 helix: 2.63 (0.20), residues: 624 sheet: -1.83 (0.93), residues: 24 loop : -0.19 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP P 214 HIS 0.003 0.001 HIS D 49 PHE 0.014 0.002 PHE F 100 TYR 0.018 0.002 TYR G 39 ARG 0.011 0.001 ARG O 213 Details of bonding type rmsd hydrogen bonds : bond 0.04467 ( 895) hydrogen bonds : angle 3.14331 ( 2235) covalent geometry : bond 0.00393 (15895) covalent geometry : angle 0.63848 (22928) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 349 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 181 MET cc_start: 0.4333 (tpt) cc_final: 0.3585 (mmt) REVERT: G 58 LEU cc_start: 0.9695 (mm) cc_final: 0.9426 (mm) REVERT: G 64 GLU cc_start: 0.9487 (OUTLIER) cc_final: 0.8855 (pp20) REVERT: G 87 ILE cc_start: 0.9559 (mt) cc_final: 0.8993 (tp) REVERT: G 88 ARG cc_start: 0.8885 (mmt180) cc_final: 0.7828 (mtp180) REVERT: G 94 ASN cc_start: 0.9290 (t0) cc_final: 0.9019 (m-40) REVERT: G 100 VAL cc_start: 0.9284 (t) cc_final: 0.8983 (p) REVERT: A 50 GLU cc_start: 0.9436 (mt-10) cc_final: 0.8794 (mt-10) REVERT: A 51 ILE cc_start: 0.8344 (mt) cc_final: 0.8007 (mt) REVERT: A 53 ARG cc_start: 0.9662 (ptm-80) cc_final: 0.9388 (ptm160) REVERT: A 59 GLU cc_start: 0.8299 (pm20) cc_final: 0.8087 (pm20) REVERT: A 73 GLU cc_start: 0.8322 (tt0) cc_final: 0.7876 (tt0) REVERT: A 81 ASP cc_start: 0.8024 (t0) cc_final: 0.7817 (t0) REVERT: A 87 SER cc_start: 0.8852 (p) cc_final: 0.8379 (t) REVERT: A 90 MET cc_start: 0.8916 (mpp) cc_final: 0.8463 (mmm) REVERT: A 94 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8436 (mm-30) REVERT: A 105 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8478 (tm-30) REVERT: A 126 LEU cc_start: 0.9545 (mm) cc_final: 0.9061 (mm) REVERT: B 25 ASN cc_start: 0.7873 (m110) cc_final: 0.7456 (m110) REVERT: B 39 ARG cc_start: 0.9222 (mmt-90) cc_final: 0.8608 (tpp-160) REVERT: B 49 LEU cc_start: 0.9527 (mm) cc_final: 0.9028 (tp) REVERT: B 84 MET cc_start: 0.9396 (mpp) cc_final: 0.9100 (mpp) REVERT: C 50 TYR cc_start: 0.8361 (t80) cc_final: 0.7837 (t80) REVERT: C 74 LYS cc_start: 0.9432 (mmtm) cc_final: 0.9134 (mmtm) REVERT: C 78 ILE cc_start: 0.8517 (mm) cc_final: 0.8236 (tp) REVERT: C 90 ASP cc_start: 0.8535 (t0) cc_final: 0.8260 (t0) REVERT: C 92 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8499 (mt-10) REVERT: D 62 MET cc_start: 0.9070 (mmm) cc_final: 0.8841 (mmm) REVERT: D 85 LYS cc_start: 0.9376 (mtpt) cc_final: 0.9076 (mmmt) REVERT: D 94 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9147 (mt) REVERT: D 101 LEU cc_start: 0.9147 (tt) cc_final: 0.8868 (tt) REVERT: E 48 LEU cc_start: 0.9252 (mt) cc_final: 0.8940 (mt) REVERT: E 50 GLU cc_start: 0.9171 (tp30) cc_final: 0.8957 (mm-30) REVERT: E 70 LEU cc_start: 0.9667 (tp) cc_final: 0.9432 (tp) REVERT: E 74 ILE cc_start: 0.9434 (mt) cc_final: 0.9150 (mt) REVERT: E 77 ASP cc_start: 0.9649 (m-30) cc_final: 0.9408 (m-30) REVERT: E 120 MET cc_start: 0.9029 (mmm) cc_final: 0.8647 (mmm) REVERT: F 44 LYS cc_start: 0.8973 (tptm) cc_final: 0.8626 (tptm) REVERT: F 63 GLU cc_start: 0.9348 (pt0) cc_final: 0.9068 (pp20) REVERT: F 84 MET cc_start: 0.9539 (tpt) cc_final: 0.9182 (tpp) REVERT: H 49 HIS cc_start: 0.8972 (m-70) cc_final: 0.8385 (m-70) REVERT: H 59 MET cc_start: 0.8996 (tpp) cc_final: 0.8768 (tpp) REVERT: H 68 ASP cc_start: 0.8922 (t0) cc_final: 0.8640 (t0) REVERT: H 69 ILE cc_start: 0.9132 (mm) cc_final: 0.8692 (mm) REVERT: H 86 ARG cc_start: 0.9005 (mmt-90) cc_final: 0.8440 (mmm-85) REVERT: H 91 SER cc_start: 0.9040 (p) cc_final: 0.8579 (p) REVERT: H 105 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8791 (mm-30) REVERT: H 109 HIS cc_start: 0.8988 (m-70) cc_final: 0.8346 (m90) REVERT: H 113 GLU cc_start: 0.9467 (mm-30) cc_final: 0.9022 (mm-30) outliers start: 2 outliers final: 0 residues processed: 350 average time/residue: 0.3095 time to fit residues: 153.0591 Evaluate side-chains 274 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 272 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 117 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 209 GLN ** O 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 211 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 82 HIS ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.072206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.051335 restraints weight = 90343.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.052441 restraints weight = 48638.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.053161 restraints weight = 32806.540| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 15895 Z= 0.313 Angle : 0.748 8.821 22928 Z= 0.436 Chirality : 0.042 0.211 2563 Planarity : 0.007 0.092 1719 Dihedral : 30.614 159.926 4918 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.90 % Favored : 96.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.27), residues: 964 helix: 1.59 (0.20), residues: 630 sheet: -1.92 (0.98), residues: 24 loop : -0.49 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP P 214 HIS 0.009 0.002 HIS F 75 PHE 0.016 0.003 PHE F 61 TYR 0.015 0.002 TYR O 259 ARG 0.008 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.07149 ( 895) hydrogen bonds : angle 3.99452 ( 2235) covalent geometry : bond 0.00680 (15895) covalent geometry : angle 0.74767 (22928) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 312 time to evaluate : 1.052 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: symmetry clash REVERT: P 181 MET cc_start: 0.4487 (tpt) cc_final: 0.3782 (mmt) REVERT: G 87 ILE cc_start: 0.9537 (mt) cc_final: 0.8985 (tp) REVERT: G 94 ASN cc_start: 0.9217 (t0) cc_final: 0.8973 (m-40) REVERT: A 50 GLU cc_start: 0.9418 (mt-10) cc_final: 0.9044 (tt0) REVERT: A 53 ARG cc_start: 0.9519 (ptm-80) cc_final: 0.9246 (ptm160) REVERT: A 54 TYR cc_start: 0.9535 (m-80) cc_final: 0.8350 (m-80) REVERT: A 73 GLU cc_start: 0.8234 (tt0) cc_final: 0.7834 (tt0) REVERT: A 87 SER cc_start: 0.9184 (p) cc_final: 0.8695 (t) REVERT: A 90 MET cc_start: 0.8901 (mpp) cc_final: 0.8443 (mmm) REVERT: A 105 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8541 (tm-30) REVERT: A 120 MET cc_start: 0.8467 (mmt) cc_final: 0.8167 (mmt) REVERT: B 25 ASN cc_start: 0.8100 (m110) cc_final: 0.7757 (m110) REVERT: B 43 VAL cc_start: 0.9296 (t) cc_final: 0.8901 (p) REVERT: B 49 LEU cc_start: 0.9467 (mm) cc_final: 0.8998 (tp) REVERT: B 63 GLU cc_start: 0.8767 (pp20) cc_final: 0.8494 (pp20) REVERT: B 68 ASP cc_start: 0.8949 (m-30) cc_final: 0.8732 (m-30) REVERT: B 84 MET cc_start: 0.9382 (mpp) cc_final: 0.9090 (mpp) REVERT: C 90 ASP cc_start: 0.8423 (t0) cc_final: 0.8135 (t0) REVERT: D 62 MET cc_start: 0.9310 (mmm) cc_final: 0.8750 (mmm) REVERT: D 98 VAL cc_start: 0.9642 (t) cc_final: 0.9431 (p) REVERT: D 101 LEU cc_start: 0.9249 (tt) cc_final: 0.9003 (tt) REVERT: D 102 LEU cc_start: 0.8910 (mt) cc_final: 0.8677 (mt) REVERT: E 50 GLU cc_start: 0.9129 (tp30) cc_final: 0.8764 (tp30) REVERT: E 60 LEU cc_start: 0.9153 (mm) cc_final: 0.8907 (mm) REVERT: E 74 ILE cc_start: 0.9480 (mt) cc_final: 0.9217 (mt) REVERT: E 77 ASP cc_start: 0.9593 (m-30) cc_final: 0.9333 (m-30) REVERT: E 93 GLN cc_start: 0.9078 (tt0) cc_final: 0.8801 (tt0) REVERT: F 25 ASN cc_start: 0.8560 (m-40) cc_final: 0.7993 (m-40) REVERT: F 58 LEU cc_start: 0.9624 (tp) cc_final: 0.9405 (tt) REVERT: F 63 GLU cc_start: 0.9264 (pt0) cc_final: 0.8898 (pp20) REVERT: F 64 ASN cc_start: 0.9625 (t0) cc_final: 0.9350 (t0) REVERT: F 84 MET cc_start: 0.9426 (tpt) cc_final: 0.9158 (tpp) REVERT: F 88 TYR cc_start: 0.9123 (m-10) cc_final: 0.8537 (m-80) REVERT: H 46 LYS cc_start: 0.9437 (ptpp) cc_final: 0.8872 (ptpp) REVERT: H 47 GLN cc_start: 0.9280 (tm-30) cc_final: 0.9024 (tm-30) REVERT: H 49 HIS cc_start: 0.8999 (m-70) cc_final: 0.8633 (m90) REVERT: H 59 MET cc_start: 0.8971 (tpp) cc_final: 0.8392 (tpp) REVERT: H 63 ASN cc_start: 0.9327 (m-40) cc_final: 0.8942 (m110) REVERT: H 82 HIS cc_start: 0.8993 (OUTLIER) cc_final: 0.8549 (m90) REVERT: H 109 HIS cc_start: 0.8939 (m-70) cc_final: 0.8088 (m-70) REVERT: H 113 GLU cc_start: 0.9324 (mm-30) cc_final: 0.8201 (mm-30) outliers start: 5 outliers final: 2 residues processed: 315 average time/residue: 0.2955 time to fit residues: 131.2148 Evaluate side-chains 252 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 249 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 23 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 215 GLN P 211 GLN G 68 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.075617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.054770 restraints weight = 86784.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.055810 restraints weight = 46754.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.056595 restraints weight = 31730.850| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4468 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= 0.181 Angle : 0.650 8.031 22928 Z= 0.383 Chirality : 0.038 0.207 2563 Planarity : 0.005 0.093 1719 Dihedral : 30.521 156.890 4918 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.70 % Favored : 97.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.27), residues: 964 helix: 1.63 (0.20), residues: 630 sheet: -1.83 (0.94), residues: 24 loop : -0.48 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 214 HIS 0.004 0.001 HIS F 75 PHE 0.018 0.002 PHE D 70 TYR 0.021 0.002 TYR P 207 ARG 0.003 0.001 ARG G 77 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 895) hydrogen bonds : angle 3.39937 ( 2235) covalent geometry : bond 0.00391 (15895) covalent geometry : angle 0.64990 (22928) *********************** 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 319 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 318 time to evaluate : 2.407 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 201 MET cc_start: 0.7825 (mpp) cc_final: 0.7420 (mpp) REVERT: P 181 MET cc_start: 0.4166 (tpt) cc_final: 0.3641 (mmp) REVERT: G 25 PHE cc_start: 0.8217 (m-10) cc_final: 0.7999 (m-10) REVERT: G 68 ASN cc_start: 0.9543 (m-40) cc_final: 0.9329 (m110) REVERT: G 87 ILE cc_start: 0.9571 (mt) cc_final: 0.9085 (tp) REVERT: A 50 GLU cc_start: 0.9451 (mt-10) cc_final: 0.8854 (mt-10) REVERT: A 51 ILE cc_start: 0.8498 (mt) cc_final: 0.8184 (mt) REVERT: A 53 ARG cc_start: 0.9483 (ptm-80) cc_final: 0.9248 (ptm160) REVERT: A 54 TYR cc_start: 0.9496 (m-80) cc_final: 0.8900 (m-80) REVERT: A 61 LEU cc_start: 0.8516 (mt) cc_final: 0.8259 (mt) REVERT: A 73 GLU cc_start: 0.8193 (tt0) cc_final: 0.7958 (tt0) REVERT: A 87 SER cc_start: 0.9130 (p) cc_final: 0.8722 (t) REVERT: A 105 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8444 (tm-30) REVERT: B 39 ARG cc_start: 0.9043 (mmt-90) cc_final: 0.8457 (tpp-160) REVERT: B 43 VAL cc_start: 0.9166 (t) cc_final: 0.8767 (p) REVERT: B 49 LEU cc_start: 0.9467 (mm) cc_final: 0.8981 (tp) REVERT: B 63 GLU cc_start: 0.8664 (pp20) cc_final: 0.8374 (pp20) REVERT: B 84 MET cc_start: 0.9354 (mpp) cc_final: 0.9075 (mpp) REVERT: C 39 TYR cc_start: 0.8919 (m-80) cc_final: 0.8099 (m-80) REVERT: C 90 ASP cc_start: 0.8283 (t0) cc_final: 0.8072 (t0) REVERT: D 34 LYS cc_start: 0.8686 (pptt) cc_final: 0.8434 (mmtp) REVERT: D 68 ASP cc_start: 0.9343 (t0) cc_final: 0.9080 (t0) REVERT: D 98 VAL cc_start: 0.9565 (t) cc_final: 0.9279 (p) REVERT: E 50 GLU cc_start: 0.9090 (tp30) cc_final: 0.8651 (tp30) REVERT: E 60 LEU cc_start: 0.9239 (mm) cc_final: 0.8774 (mm) REVERT: E 73 GLU cc_start: 0.9278 (pt0) cc_final: 0.8227 (pt0) REVERT: E 74 ILE cc_start: 0.9486 (mt) cc_final: 0.9184 (mt) REVERT: E 77 ASP cc_start: 0.9499 (m-30) cc_final: 0.9200 (m-30) REVERT: E 90 MET cc_start: 0.9351 (mmm) cc_final: 0.8962 (mmp) REVERT: E 120 MET cc_start: 0.9148 (mmm) cc_final: 0.8484 (mmm) REVERT: F 63 GLU cc_start: 0.9232 (pt0) cc_final: 0.8830 (pp20) REVERT: F 64 ASN cc_start: 0.9593 (t0) cc_final: 0.9293 (t0) REVERT: F 84 MET cc_start: 0.9269 (tpt) cc_final: 0.8837 (tpp) REVERT: H 46 LYS cc_start: 0.9472 (ptpp) cc_final: 0.8828 (ptpp) REVERT: H 47 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8892 (tm-30) REVERT: H 59 MET cc_start: 0.8824 (tpp) cc_final: 0.8542 (tpp) REVERT: H 109 HIS cc_start: 0.8785 (m-70) cc_final: 0.8189 (m-70) REVERT: H 113 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8565 (mm-30) REVERT: H 116 LYS cc_start: 0.9415 (pttm) cc_final: 0.9150 (pttm) outliers start: 1 outliers final: 0 residues processed: 318 average time/residue: 0.3016 time to fit residues: 137.4806 Evaluate side-chains 261 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 81 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.074469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.053994 restraints weight = 89146.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.054955 restraints weight = 48420.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.055770 restraints weight = 32927.408| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4852 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= 0.205 Angle : 0.656 8.234 22928 Z= 0.387 Chirality : 0.038 0.195 2563 Planarity : 0.005 0.094 1719 Dihedral : 30.505 154.611 4918 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.22 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.27), residues: 964 helix: 1.55 (0.20), residues: 630 sheet: -1.92 (0.95), residues: 24 loop : -0.48 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 214 HIS 0.005 0.001 HIS F 75 PHE 0.013 0.002 PHE D 70 TYR 0.019 0.002 TYR C 50 ARG 0.010 0.001 ARG O 219 Details of bonding type rmsd hydrogen bonds : bond 0.04764 ( 895) hydrogen bonds : angle 3.47133 ( 2235) covalent geometry : bond 0.00443 (15895) covalent geometry : angle 0.65580 (22928) *********************** 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 302 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 193 LEU cc_start: 0.9217 (tp) cc_final: 0.8472 (tp) REVERT: O 197 TYR cc_start: 0.8509 (m-10) cc_final: 0.8289 (m-80) REVERT: O 201 MET cc_start: 0.7684 (mpp) cc_final: 0.7135 (mpp) REVERT: P 181 MET cc_start: 0.4067 (tpt) cc_final: 0.3436 (mmt) REVERT: G 38 ASN cc_start: 0.9184 (t0) cc_final: 0.8978 (t0) REVERT: G 39 TYR cc_start: 0.8827 (m-80) cc_final: 0.8614 (m-80) REVERT: G 56 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8735 (tm-30) REVERT: G 88 ARG cc_start: 0.8632 (mmt180) cc_final: 0.7490 (mtp180) REVERT: A 53 ARG cc_start: 0.9485 (ptm-80) cc_final: 0.9274 (ptm160) REVERT: A 54 TYR cc_start: 0.9512 (m-80) cc_final: 0.8856 (m-80) REVERT: A 87 SER cc_start: 0.9116 (p) cc_final: 0.8680 (t) REVERT: A 90 MET cc_start: 0.8799 (mpp) cc_final: 0.8431 (mmm) REVERT: A 105 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8480 (tm-30) REVERT: B 43 VAL cc_start: 0.9175 (t) cc_final: 0.8743 (p) REVERT: B 49 LEU cc_start: 0.9387 (mm) cc_final: 0.8955 (tp) REVERT: B 63 GLU cc_start: 0.8714 (pp20) cc_final: 0.8460 (pp20) REVERT: B 84 MET cc_start: 0.9354 (mpp) cc_final: 0.9067 (mpp) REVERT: C 36 LYS cc_start: 0.9445 (mmtm) cc_final: 0.8989 (mtmt) REVERT: C 39 TYR cc_start: 0.8716 (m-80) cc_final: 0.8225 (m-80) REVERT: C 90 ASP cc_start: 0.8527 (t0) cc_final: 0.8260 (t0) REVERT: D 62 MET cc_start: 0.9129 (mmm) cc_final: 0.8755 (mmm) REVERT: D 83 TYR cc_start: 0.8460 (m-10) cc_final: 0.7593 (m-10) REVERT: D 85 LYS cc_start: 0.9458 (mtpt) cc_final: 0.8964 (mmmt) REVERT: D 96 THR cc_start: 0.9614 (m) cc_final: 0.9191 (p) REVERT: E 50 GLU cc_start: 0.9066 (tp30) cc_final: 0.8604 (tp30) REVERT: E 60 LEU cc_start: 0.9194 (mm) cc_final: 0.8881 (mm) REVERT: E 74 ILE cc_start: 0.9494 (mt) cc_final: 0.9175 (mt) REVERT: E 77 ASP cc_start: 0.9501 (m-30) cc_final: 0.9215 (m-30) REVERT: E 82 LEU cc_start: 0.7846 (mt) cc_final: 0.7514 (mt) REVERT: E 90 MET cc_start: 0.9390 (mmm) cc_final: 0.9047 (mmp) REVERT: E 93 GLN cc_start: 0.8889 (tt0) cc_final: 0.8613 (tt0) REVERT: E 120 MET cc_start: 0.9176 (mmm) cc_final: 0.8504 (mmm) REVERT: F 63 GLU cc_start: 0.9245 (pt0) cc_final: 0.8850 (pp20) REVERT: F 64 ASN cc_start: 0.9606 (t0) cc_final: 0.9334 (t0) REVERT: F 84 MET cc_start: 0.9233 (tpt) cc_final: 0.8978 (tpp) REVERT: H 46 LYS cc_start: 0.9546 (ptpp) cc_final: 0.9346 (mmtt) REVERT: H 47 GLN cc_start: 0.9231 (tm-30) cc_final: 0.8936 (tm-30) REVERT: H 76 GLU cc_start: 0.8783 (mp0) cc_final: 0.8262 (mp0) REVERT: H 109 HIS cc_start: 0.8970 (m-70) cc_final: 0.8100 (m-70) REVERT: H 113 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8574 (mm-30) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.2934 time to fit residues: 124.9305 Evaluate side-chains 248 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 75 optimal weight: 0.0470 chunk 100 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** B 25 ASN ** 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 82 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.077199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.056076 restraints weight = 85914.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.057165 restraints weight = 46935.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.057917 restraints weight = 31723.948| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15895 Z= 0.160 Angle : 0.642 8.401 22928 Z= 0.378 Chirality : 0.037 0.178 2563 Planarity : 0.005 0.094 1719 Dihedral : 30.369 150.346 4918 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.80 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.27), residues: 964 helix: 1.54 (0.20), residues: 628 sheet: -1.80 (0.94), residues: 24 loop : -0.43 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 214 HIS 0.008 0.001 HIS D 109 PHE 0.014 0.001 PHE E 67 TYR 0.021 0.002 TYR H 40 ARG 0.008 0.001 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 895) hydrogen bonds : angle 3.23651 ( 2235) covalent geometry : bond 0.00340 (15895) covalent geometry : angle 0.64213 (22928) *********************** 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 309 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 1.057 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: 0.7908 (mpp) cc_final: 0.7566 (mpp) REVERT: P 181 MET cc_start: 0.4112 (tpt) cc_final: 0.3553 (mmp) REVERT: G 56 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8547 (tm-30) REVERT: G 68 ASN cc_start: 0.9530 (m-40) cc_final: 0.9297 (m110) REVERT: G 88 ARG cc_start: 0.8621 (mmt180) cc_final: 0.7517 (mtp180) REVERT: A 50 GLU cc_start: 0.9505 (mt-10) cc_final: 0.9144 (mt-10) REVERT: A 53 ARG cc_start: 0.9451 (ptm-80) cc_final: 0.9240 (ptm160) REVERT: A 54 TYR cc_start: 0.9482 (m-80) cc_final: 0.9010 (m-80) REVERT: A 87 SER cc_start: 0.8953 (p) cc_final: 0.8504 (t) REVERT: A 90 MET cc_start: 0.8851 (mpp) cc_final: 0.8533 (mmm) REVERT: A 105 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8387 (tm-30) REVERT: A 120 MET cc_start: 0.8815 (mmt) cc_final: 0.8598 (mmt) REVERT: A 130 ILE cc_start: 0.9405 (mm) cc_final: 0.9050 (mm) REVERT: B 49 LEU cc_start: 0.9427 (mm) cc_final: 0.8850 (tp) REVERT: B 52 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8582 (mp0) REVERT: B 63 GLU cc_start: 0.8737 (pp20) cc_final: 0.8451 (pp20) REVERT: C 39 TYR cc_start: 0.8691 (m-80) cc_final: 0.8205 (m-80) REVERT: C 84 GLN cc_start: 0.9037 (tp-100) cc_final: 0.8836 (tp-100) REVERT: C 90 ASP cc_start: 0.8401 (t0) cc_final: 0.7976 (t0) REVERT: D 34 LYS cc_start: 0.8684 (pptt) cc_final: 0.8458 (mmtp) REVERT: D 76 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8686 (mm-30) REVERT: D 96 THR cc_start: 0.9568 (m) cc_final: 0.9347 (p) REVERT: E 48 LEU cc_start: 0.9356 (mt) cc_final: 0.9127 (mt) REVERT: E 50 GLU cc_start: 0.9025 (tp30) cc_final: 0.8604 (tp30) REVERT: E 77 ASP cc_start: 0.9476 (m-30) cc_final: 0.9200 (m-30) REVERT: E 82 LEU cc_start: 0.7862 (mt) cc_final: 0.7348 (mt) REVERT: E 90 MET cc_start: 0.9384 (mmm) cc_final: 0.8968 (mmp) REVERT: E 93 GLN cc_start: 0.8686 (tt0) cc_final: 0.8436 (tt0) REVERT: E 105 GLU cc_start: 0.8792 (pp20) cc_final: 0.8503 (pp20) REVERT: E 120 MET cc_start: 0.9150 (mmm) cc_final: 0.8425 (mmm) REVERT: F 49 LEU cc_start: 0.9320 (mt) cc_final: 0.9119 (mt) REVERT: F 63 GLU cc_start: 0.9247 (pt0) cc_final: 0.8852 (pp20) REVERT: F 64 ASN cc_start: 0.9618 (t0) cc_final: 0.9325 (t0) REVERT: F 66 ILE cc_start: 0.9625 (mm) cc_final: 0.9276 (mt) REVERT: H 46 LYS cc_start: 0.9525 (ptpp) cc_final: 0.9097 (pttm) REVERT: H 47 GLN cc_start: 0.9231 (tm-30) cc_final: 0.9020 (tm-30) REVERT: H 69 ILE cc_start: 0.8862 (mm) cc_final: 0.8535 (mm) REVERT: H 86 ARG cc_start: 0.8866 (mmt-90) cc_final: 0.8593 (mmm-85) REVERT: H 109 HIS cc_start: 0.8982 (m-70) cc_final: 0.8099 (m-70) REVERT: H 113 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8537 (mm-30) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.2845 time to fit residues: 124.1336 Evaluate side-chains 254 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 63 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 111 optimal weight: 0.3980 chunk 66 optimal weight: 5.9990 chunk 55 optimal weight: 0.0050 chunk 41 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.077430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.057037 restraints weight = 83989.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.058245 restraints weight = 44547.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.059058 restraints weight = 29727.376| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15895 Z= 0.158 Angle : 0.634 11.591 22928 Z= 0.372 Chirality : 0.036 0.174 2563 Planarity : 0.005 0.095 1719 Dihedral : 30.271 149.747 4918 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.01 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.27), residues: 964 helix: 1.47 (0.20), residues: 627 sheet: -1.58 (0.99), residues: 24 loop : -0.46 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 214 HIS 0.004 0.001 HIS D 109 PHE 0.021 0.002 PHE F 61 TYR 0.021 0.002 TYR H 40 ARG 0.006 0.000 ARG C 77 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 895) hydrogen bonds : angle 3.25444 ( 2235) covalent geometry : bond 0.00337 (15895) covalent geometry : angle 0.63377 (22928) *********************** 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 300 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.224 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: 0.4191 (tpt) cc_final: 0.3594 (mmp) REVERT: G 56 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8575 (tm-30) REVERT: G 88 ARG cc_start: 0.8627 (mmt180) cc_final: 0.7455 (mtp180) REVERT: A 50 GLU cc_start: 0.9503 (mt-10) cc_final: 0.9139 (mt-10) REVERT: A 53 ARG cc_start: 0.9473 (ptm-80) cc_final: 0.9232 (ptm160) REVERT: A 54 TYR cc_start: 0.9407 (m-80) cc_final: 0.8982 (m-80) REVERT: A 87 SER cc_start: 0.8925 (p) cc_final: 0.8493 (t) REVERT: A 90 MET cc_start: 0.8895 (mpp) cc_final: 0.8549 (mmm) REVERT: A 94 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8226 (mt-10) REVERT: A 105 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8430 (tm-30) REVERT: A 120 MET cc_start: 0.8835 (mmt) cc_final: 0.8612 (mmm) REVERT: A 126 LEU cc_start: 0.9749 (tp) cc_final: 0.9534 (mm) REVERT: B 49 LEU cc_start: 0.9465 (mm) cc_final: 0.8856 (tp) REVERT: B 63 GLU cc_start: 0.8744 (pp20) cc_final: 0.8490 (pp20) REVERT: B 68 ASP cc_start: 0.8837 (m-30) cc_final: 0.8528 (m-30) REVERT: C 36 LYS cc_start: 0.9316 (mmtm) cc_final: 0.8926 (mtmt) REVERT: C 39 TYR cc_start: 0.8646 (m-80) cc_final: 0.8203 (m-80) REVERT: C 90 ASP cc_start: 0.8515 (t0) cc_final: 0.8195 (t0) REVERT: D 76 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8709 (mm-30) REVERT: D 96 THR cc_start: 0.9535 (m) cc_final: 0.9332 (p) REVERT: D 116 LYS cc_start: 0.9210 (ptpp) cc_final: 0.8914 (ptpp) REVERT: E 50 GLU cc_start: 0.9021 (tp30) cc_final: 0.8570 (tp30) REVERT: E 77 ASP cc_start: 0.9463 (m-30) cc_final: 0.9197 (m-30) REVERT: E 82 LEU cc_start: 0.7677 (mt) cc_final: 0.7320 (mt) REVERT: E 90 MET cc_start: 0.9436 (mmm) cc_final: 0.9216 (mmp) REVERT: E 105 GLU cc_start: 0.8887 (pp20) cc_final: 0.8532 (pp20) REVERT: E 120 MET cc_start: 0.9023 (mmm) cc_final: 0.8475 (mmm) REVERT: F 49 LEU cc_start: 0.9444 (mt) cc_final: 0.9177 (mt) REVERT: F 63 GLU cc_start: 0.9307 (pt0) cc_final: 0.8803 (pp20) REVERT: F 64 ASN cc_start: 0.9597 (t0) cc_final: 0.9294 (t0) REVERT: F 66 ILE cc_start: 0.9545 (mm) cc_final: 0.9194 (mt) REVERT: F 84 MET cc_start: 0.9342 (tpt) cc_final: 0.9093 (tpp) REVERT: H 34 LYS cc_start: 0.9049 (mmmm) cc_final: 0.8810 (mptt) REVERT: H 46 LYS cc_start: 0.9515 (ptpp) cc_final: 0.9060 (pttm) REVERT: H 59 MET cc_start: 0.8748 (tpp) cc_final: 0.8470 (tpt) REVERT: H 69 ILE cc_start: 0.8840 (mm) cc_final: 0.8486 (mm) REVERT: H 86 ARG cc_start: 0.8810 (mmt-90) cc_final: 0.8504 (mmm-85) REVERT: H 109 HIS cc_start: 0.8993 (m-70) cc_final: 0.8160 (m-70) REVERT: H 113 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8534 (mm-30) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2918 time to fit residues: 123.8532 Evaluate side-chains 256 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 61 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 18 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.075104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.054220 restraints weight = 87672.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.055331 restraints weight = 47984.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.056116 restraints weight = 33299.061| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15895 Z= 0.198 Angle : 0.660 10.467 22928 Z= 0.388 Chirality : 0.037 0.174 2563 Planarity : 0.006 0.119 1719 Dihedral : 30.399 151.386 4918 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.42 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.27), residues: 964 helix: 1.40 (0.20), residues: 628 sheet: -1.66 (0.98), residues: 24 loop : -0.48 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 214 HIS 0.009 0.001 HIS P 220 PHE 0.012 0.001 PHE D 65 TYR 0.021 0.002 TYR B 88 ARG 0.008 0.001 ARG G 11 Details of bonding type rmsd hydrogen bonds : bond 0.04551 ( 895) hydrogen bonds : angle 3.43087 ( 2235) covalent geometry : bond 0.00428 (15895) covalent geometry : angle 0.66007 (22928) *********************** 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 293 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 201 MET cc_start: 0.8032 (mpp) cc_final: 0.7617 (mpp) REVERT: P 181 MET cc_start: 0.4191 (tpt) cc_final: 0.3627 (mmt) REVERT: G 11 ARG cc_start: 0.7606 (tpp80) cc_final: 0.7297 (mmm-85) REVERT: G 56 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8535 (tm-30) REVERT: G 68 ASN cc_start: 0.9506 (m-40) cc_final: 0.9195 (m110) REVERT: A 50 GLU cc_start: 0.9515 (mt-10) cc_final: 0.9124 (mt-10) REVERT: A 53 ARG cc_start: 0.9482 (ptm-80) cc_final: 0.9266 (ptm160) REVERT: A 54 TYR cc_start: 0.9448 (m-80) cc_final: 0.8977 (m-80) REVERT: A 61 LEU cc_start: 0.8315 (mt) cc_final: 0.8102 (mt) REVERT: A 87 SER cc_start: 0.9026 (p) cc_final: 0.8569 (t) REVERT: A 90 MET cc_start: 0.8892 (mpp) cc_final: 0.8573 (mmm) REVERT: A 94 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8209 (mt-10) REVERT: A 120 MET cc_start: 0.8757 (mmt) cc_final: 0.8465 (mmt) REVERT: A 126 LEU cc_start: 0.9786 (tp) cc_final: 0.9513 (mm) REVERT: B 63 GLU cc_start: 0.8709 (pp20) cc_final: 0.8502 (pp20) REVERT: C 90 ASP cc_start: 0.8599 (t0) cc_final: 0.8274 (t0) REVERT: D 76 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8620 (mm-30) REVERT: D 85 LYS cc_start: 0.9439 (mtpt) cc_final: 0.9020 (mmmt) REVERT: E 50 GLU cc_start: 0.9049 (tp30) cc_final: 0.8523 (tp30) REVERT: E 77 ASP cc_start: 0.9477 (m-30) cc_final: 0.9227 (m-30) REVERT: E 90 MET cc_start: 0.9343 (mmm) cc_final: 0.9057 (mmm) REVERT: E 93 GLN cc_start: 0.8878 (tt0) cc_final: 0.8663 (tt0) REVERT: E 119 ILE cc_start: 0.9482 (pt) cc_final: 0.9252 (pt) REVERT: E 120 MET cc_start: 0.9123 (mmm) cc_final: 0.8406 (mmm) REVERT: F 63 GLU cc_start: 0.9267 (pt0) cc_final: 0.8784 (pp20) REVERT: F 64 ASN cc_start: 0.9586 (t0) cc_final: 0.9317 (t0) REVERT: F 66 ILE cc_start: 0.9548 (mm) cc_final: 0.9215 (mt) REVERT: F 84 MET cc_start: 0.9164 (tpt) cc_final: 0.8918 (tpp) REVERT: H 42 TYR cc_start: 0.7034 (t80) cc_final: 0.6823 (t80) REVERT: H 46 LYS cc_start: 0.9518 (ptpp) cc_final: 0.9182 (pttm) REVERT: H 69 ILE cc_start: 0.8850 (mm) cc_final: 0.8497 (mm) REVERT: H 76 GLU cc_start: 0.8871 (mp0) cc_final: 0.8667 (mp0) REVERT: H 86 ARG cc_start: 0.9006 (mmt-90) cc_final: 0.8636 (ttm-80) REVERT: H 109 HIS cc_start: 0.8974 (m-70) cc_final: 0.8058 (m-70) REVERT: H 113 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8549 (mm-30) REVERT: H 116 LYS cc_start: 0.9131 (pttm) cc_final: 0.8880 (pttm) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.2971 time to fit residues: 123.6238 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 : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 111 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 chunk 110 optimal weight: 0.0980 chunk 64 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.076363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.056011 restraints weight = 84145.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.057166 restraints weight = 45632.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.057960 restraints weight = 30812.920| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15895 Z= 0.167 Angle : 0.648 9.157 22928 Z= 0.380 Chirality : 0.037 0.182 2563 Planarity : 0.005 0.095 1719 Dihedral : 30.328 149.904 4918 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.32 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.27), residues: 964 helix: 1.40 (0.20), residues: 628 sheet: -1.48 (1.02), residues: 24 loop : -0.48 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 214 HIS 0.004 0.001 HIS P 220 PHE 0.019 0.001 PHE D 65 TYR 0.022 0.002 TYR H 40 ARG 0.005 0.000 ARG C 77 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 895) hydrogen bonds : angle 3.33618 ( 2235) covalent geometry : bond 0.00360 (15895) covalent geometry : angle 0.64778 (22928) *********************** 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 286 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 1.064 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 183 ILE cc_start: 0.5333 (mt) cc_final: 0.5132 (mt) REVERT: O 201 MET cc_start: 0.7989 (mpp) cc_final: 0.7718 (mpp) REVERT: P 181 MET cc_start: 0.4270 (tpt) cc_final: 0.3672 (mmt) REVERT: G 56 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8530 (tm-30) REVERT: G 68 ASN cc_start: 0.9522 (m-40) cc_final: 0.9189 (p0) REVERT: A 50 GLU cc_start: 0.9516 (mt-10) cc_final: 0.9134 (mt-10) REVERT: A 53 ARG cc_start: 0.9454 (ptm-80) cc_final: 0.9240 (ptm160) REVERT: A 54 TYR cc_start: 0.9413 (m-80) cc_final: 0.9056 (m-80) REVERT: A 87 SER cc_start: 0.8973 (p) cc_final: 0.8513 (t) REVERT: A 90 MET cc_start: 0.8927 (mpp) cc_final: 0.8584 (mmm) REVERT: A 94 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8133 (mt-10) REVERT: A 105 GLU cc_start: 0.8583 (tt0) cc_final: 0.8302 (pp20) REVERT: A 120 MET cc_start: 0.8656 (mmt) cc_final: 0.8418 (mmm) REVERT: A 126 LEU cc_start: 0.9766 (tp) cc_final: 0.9531 (mm) REVERT: B 49 LEU cc_start: 0.9490 (mm) cc_final: 0.8902 (tp) REVERT: B 63 GLU cc_start: 0.8750 (pp20) cc_final: 0.8512 (pp20) REVERT: C 36 LYS cc_start: 0.9373 (mmtm) cc_final: 0.9087 (mtmt) REVERT: C 84 GLN cc_start: 0.9068 (tp-100) cc_final: 0.8855 (tp-100) REVERT: C 90 ASP cc_start: 0.8554 (t0) cc_final: 0.8234 (t0) REVERT: D 34 LYS cc_start: 0.8617 (pptt) cc_final: 0.8358 (mmtp) REVERT: D 76 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8678 (mm-30) REVERT: D 85 LYS cc_start: 0.9442 (mtpt) cc_final: 0.9017 (mmmt) REVERT: E 50 GLU cc_start: 0.9029 (tp30) cc_final: 0.8592 (tp30) REVERT: E 77 ASP cc_start: 0.9417 (m-30) cc_final: 0.9181 (m-30) REVERT: E 90 MET cc_start: 0.9387 (mmm) cc_final: 0.9104 (mmm) REVERT: E 106 ASP cc_start: 0.9048 (m-30) cc_final: 0.8714 (m-30) REVERT: E 120 MET cc_start: 0.9142 (mmm) cc_final: 0.8367 (mmm) REVERT: F 49 LEU cc_start: 0.9371 (mt) cc_final: 0.9166 (mt) REVERT: F 63 GLU cc_start: 0.9290 (pt0) cc_final: 0.8795 (pp20) REVERT: F 64 ASN cc_start: 0.9593 (t0) cc_final: 0.9275 (t0) REVERT: F 66 ILE cc_start: 0.9534 (mm) cc_final: 0.9193 (mt) REVERT: F 84 MET cc_start: 0.8995 (tpt) cc_final: 0.8767 (tpp) REVERT: H 34 LYS cc_start: 0.9111 (mmmm) cc_final: 0.8845 (mptt) REVERT: H 42 TYR cc_start: 0.7007 (t80) cc_final: 0.6740 (t80) REVERT: H 46 LYS cc_start: 0.9536 (ptpp) cc_final: 0.9232 (pttm) REVERT: H 59 MET cc_start: 0.8752 (tpp) cc_final: 0.8521 (tpt) REVERT: H 69 ILE cc_start: 0.8847 (mm) cc_final: 0.8484 (mm) REVERT: H 76 GLU cc_start: 0.8896 (mp0) cc_final: 0.8577 (mp0) REVERT: H 86 ARG cc_start: 0.8979 (mmt-90) cc_final: 0.8567 (ttm-80) REVERT: H 109 HIS cc_start: 0.9024 (m-70) cc_final: 0.8120 (m-70) REVERT: H 113 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8546 (mm-30) REVERT: H 116 LYS cc_start: 0.9145 (pttm) cc_final: 0.8917 (pttm) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.2825 time to fit residues: 115.3014 Evaluate side-chains 245 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 114 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 119 optimal weight: 0.4980 chunk 82 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.073259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.052369 restraints weight = 89874.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.053423 restraints weight = 49811.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.054168 restraints weight = 34362.679| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.5947 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= 0.232 Angle : 0.694 8.128 22928 Z= 0.407 Chirality : 0.039 0.189 2563 Planarity : 0.006 0.096 1719 Dihedral : 30.579 151.777 4918 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.05 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.27), residues: 964 helix: 1.29 (0.20), residues: 625 sheet: -1.79 (0.99), residues: 24 loop : -0.58 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP P 244 HIS 0.005 0.001 HIS F 75 PHE 0.017 0.002 PHE D 65 TYR 0.024 0.002 TYR H 40 ARG 0.011 0.001 ARG O 219 Details of bonding type rmsd hydrogen bonds : bond 0.05293 ( 895) hydrogen bonds : angle 3.61042 ( 2235) covalent geometry : bond 0.00503 (15895) covalent geometry : angle 0.69427 (22928) ********************** 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 285 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.213 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 183 ILE cc_start: 0.4885 (mt) cc_final: 0.4672 (mt) REVERT: O 201 MET cc_start: 0.7904 (mpp) cc_final: 0.7618 (mpp) REVERT: G 56 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8541 (tm-30) REVERT: G 68 ASN cc_start: 0.9527 (m-40) cc_final: 0.9305 (m110) REVERT: G 104 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8545 (tm-30) REVERT: A 50 GLU cc_start: 0.9529 (mt-10) cc_final: 0.9106 (mt-10) REVERT: A 53 ARG cc_start: 0.9512 (ptm-80) cc_final: 0.9221 (ptm160) REVERT: A 54 TYR cc_start: 0.9482 (m-80) cc_final: 0.8932 (m-80) REVERT: A 87 SER cc_start: 0.9123 (p) cc_final: 0.8640 (t) REVERT: A 94 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8216 (mm-30) REVERT: A 120 MET cc_start: 0.8679 (mmt) cc_final: 0.8351 (mmt) REVERT: A 126 LEU cc_start: 0.9798 (tp) cc_final: 0.9489 (mm) REVERT: A 130 ILE cc_start: 0.9416 (mm) cc_final: 0.9138 (mm) REVERT: B 43 VAL cc_start: 0.9210 (t) cc_final: 0.8771 (p) REVERT: B 63 GLU cc_start: 0.8749 (pp20) cc_final: 0.8527 (pp20) REVERT: B 93 GLN cc_start: 0.8403 (pp30) cc_final: 0.8059 (pp30) REVERT: C 84 GLN cc_start: 0.9045 (tp-100) cc_final: 0.8841 (tp-100) REVERT: C 90 ASP cc_start: 0.8564 (t0) cc_final: 0.8250 (t0) REVERT: D 76 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8600 (mm-30) REVERT: D 109 HIS cc_start: 0.8940 (m-70) cc_final: 0.8424 (m170) REVERT: E 50 GLU cc_start: 0.9061 (tp30) cc_final: 0.8561 (tp30) REVERT: E 77 ASP cc_start: 0.9384 (m-30) cc_final: 0.9174 (m-30) REVERT: E 90 MET cc_start: 0.9354 (mmm) cc_final: 0.8970 (mmp) REVERT: E 93 GLN cc_start: 0.8823 (tt0) cc_final: 0.8497 (tt0) REVERT: E 120 MET cc_start: 0.9163 (mmm) cc_final: 0.8447 (mmm) REVERT: F 63 GLU cc_start: 0.9275 (pt0) cc_final: 0.8782 (pp20) REVERT: F 64 ASN cc_start: 0.9602 (t0) cc_final: 0.9319 (t0) REVERT: F 66 ILE cc_start: 0.9540 (mm) cc_final: 0.9205 (mt) REVERT: F 68 ASP cc_start: 0.9093 (m-30) cc_final: 0.8890 (m-30) REVERT: F 84 MET cc_start: 0.8884 (tpt) cc_final: 0.8681 (tpp) REVERT: H 37 TYR cc_start: 0.8983 (m-80) cc_final: 0.8649 (m-10) REVERT: H 59 MET cc_start: 0.8713 (tpp) cc_final: 0.8435 (tpt) REVERT: H 69 ILE cc_start: 0.8902 (mm) cc_final: 0.8562 (mm) REVERT: H 76 GLU cc_start: 0.8800 (mp0) cc_final: 0.8573 (mp0) REVERT: H 86 ARG cc_start: 0.9056 (mmt-90) cc_final: 0.8646 (ttm-80) REVERT: H 109 HIS cc_start: 0.9019 (m-70) cc_final: 0.8136 (m-70) REVERT: H 113 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8515 (mm-30) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.2968 time to fit residues: 119.4807 Evaluate side-chains 243 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 107 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 69 optimal weight: 0.0970 chunk 59 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 81 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 220 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.076730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.055762 restraints weight = 87660.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.056995 restraints weight = 48642.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.057805 restraints weight = 33023.555| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15895 Z= 0.162 Angle : 0.660 8.700 22928 Z= 0.385 Chirality : 0.037 0.173 2563 Planarity : 0.005 0.095 1719 Dihedral : 30.369 150.395 4918 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.53 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.27), residues: 964 helix: 1.40 (0.20), residues: 625 sheet: -1.44 (1.07), residues: 24 loop : -0.57 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP O 214 HIS 0.003 0.001 HIS D 109 PHE 0.019 0.001 PHE D 65 TYR 0.022 0.002 TYR H 40 ARG 0.008 0.000 ARG H 79 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 895) hydrogen bonds : angle 3.30295 ( 2235) covalent geometry : bond 0.00345 (15895) covalent geometry : angle 0.65953 (22928) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4904.79 seconds wall clock time: 85 minutes 52.61 seconds (5152.61 seconds total)