Starting phenix.real_space_refine on Thu Oct 22 19:53:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xjk_66938/10_2026/9xjk_66938.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xjk_66938/10_2026/9xjk_66938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xjk_66938/10_2026/9xjk_66938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xjk_66938/10_2026/9xjk_66938.map" model { file = "/net/cci-nas-00/data/ceres_data/9xjk_66938/10_2026/9xjk_66938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xjk_66938/10_2026/9xjk_66938.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2841 2.51 5 N 773 2.21 5 O 933 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4568 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1294 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 4, 'TRANS': 169} Chain: "B" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1653 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 212} Chain: "C" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1621 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 201} Time building chain proxies: 1.14, per 1000 atoms: 0.25 Number of scatterers: 4568 At special positions: 0 Unit cell: (59.792, 67.064, 124.432, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 933 8.00 N 773 7.00 C 2841 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 57 " distance=2.02 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 158 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 149 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 90 " distance=2.04 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 199 " distance=2.03 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: 0.36 Conformation dependent library (CDL) restraints added in 167.2 milliseconds 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1132 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 14 sheets defined 22.7% alpha, 43.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 2 through 26 Processing helix chain 'A' and resid 60 through 79 removed outlier: 3.599A pdb=" N GLN A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 96 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 103 through 117 removed outlier: 3.642A pdb=" N ASN A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 153 through 170 Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.584A pdb=" N THR B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 removed outlier: 4.357A pdb=" N GLY B 108 " --> pdb=" O TYR B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 196 through 201 removed outlier: 3.800A pdb=" N THR B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.522A pdb=" N GLU C 85 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 133 removed outlier: 4.199A pdb=" N GLN C 132 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA C 133 " --> pdb=" O GLU C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 194 removed outlier: 3.611A pdb=" N HIS C 194 " --> pdb=" O GLN C 190 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 45 removed outlier: 3.518A pdb=" N GLN A 129 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL A 131 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE A 41 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE A 133 " --> pdb=" O PHE A 41 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE A 43 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU A 135 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLN A 45 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.645A pdb=" N ASN A 50 " --> pdb=" O THR A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.943A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 59 removed outlier: 6.661A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 59 removed outlier: 6.661A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 129 through 133 removed outlier: 5.508A pdb=" N ALA B 146 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B 193 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLY B 148 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL B 191 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU B 150 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N SER B 189 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LYS B 152 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU B 187 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 129 through 133 removed outlier: 5.508A pdb=" N ALA B 146 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B 193 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLY B 148 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL B 191 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU B 150 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N SER B 189 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LYS B 152 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU B 187 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 160 through 163 Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AB1, first strand: chain 'C' and resid 9 through 12 removed outlier: 7.028A pdb=" N VAL C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 9 through 12 removed outlier: 7.028A pdb=" N VAL C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.591A pdb=" N VAL C 139 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA C 136 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TYR C 178 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.591A pdb=" N VAL C 139 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA C 136 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TYR C 178 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 159 through 161 removed outlier: 4.384A pdb=" N TRP C 154 " --> pdb=" O VAL C 161 " (cutoff:3.500A) 237 hydrogen bonds defined for protein. 627 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.74 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1500 1.34 - 1.46: 1050 1.46 - 1.58: 2080 1.58 - 1.70: 0 1.70 - 1.81: 26 Bond restraints: 4656 Sorted by residual: bond pdb=" CG PRO C 125 " pdb=" CD PRO C 125 " ideal model delta sigma weight residual 1.503 1.565 -0.062 3.40e-02 8.65e+02 3.32e+00 bond pdb=" N PRO C 125 " pdb=" CA PRO C 125 " ideal model delta sigma weight residual 1.465 1.435 0.030 2.03e-02 2.43e+03 2.18e+00 bond pdb=" CB PRO C 125 " pdb=" CG PRO C 125 " ideal model delta sigma weight residual 1.492 1.549 -0.057 5.00e-02 4.00e+02 1.28e+00 bond pdb=" CB GLN B 114 " pdb=" CG GLN B 114 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" CG MET B 34 " pdb=" SD MET B 34 " ideal model delta sigma weight residual 1.803 1.778 0.025 2.50e-02 1.60e+03 1.02e+00 ... (remaining 4651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 6216 2.00 - 3.99: 99 3.99 - 5.99: 23 5.99 - 7.98: 4 7.98 - 9.98: 2 Bond angle restraints: 6344 Sorted by residual: angle pdb=" CA PRO C 125 " pdb=" N PRO C 125 " pdb=" CD PRO C 125 " ideal model delta sigma weight residual 112.00 106.26 5.74 1.40e+00 5.10e-01 1.68e+01 angle pdb=" C SER C 96 " pdb=" N LEU C 97 " pdb=" CA LEU C 97 " ideal model delta sigma weight residual 121.54 128.59 -7.05 1.91e+00 2.74e-01 1.36e+01 angle pdb=" N ALA B 91 " pdb=" CA ALA B 91 " pdb=" C ALA B 91 " ideal model delta sigma weight residual 107.73 112.17 -4.44 1.34e+00 5.57e-01 1.10e+01 angle pdb=" C ALA A 85 " pdb=" N TYR A 86 " pdb=" CA TYR A 86 " ideal model delta sigma weight residual 122.67 118.08 4.59 1.59e+00 3.96e-01 8.35e+00 angle pdb=" CA LEU C 97 " pdb=" CB LEU C 97 " pdb=" CG LEU C 97 " ideal model delta sigma weight residual 116.30 126.28 -9.98 3.50e+00 8.16e-02 8.13e+00 ... (remaining 6339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 2484 16.87 - 33.73: 268 33.73 - 50.60: 48 50.60 - 67.46: 9 67.46 - 84.32: 7 Dihedral angle restraints: 2816 sinusoidal: 1045 harmonic: 1771 Sorted by residual: dihedral pdb=" CA GLU C 52 " pdb=" C GLU C 52 " pdb=" N ASN C 53 " pdb=" CA ASN C 53 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASN A 130 " pdb=" CB ASN A 130 " pdb=" CG ASN A 130 " pdb=" OD1 ASN A 130 " ideal model delta sinusoidal sigma weight residual 120.00 -167.50 -72.50 2 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA TYR A 86 " pdb=" C TYR A 86 " pdb=" N VAL A 87 " pdb=" CA VAL A 87 " ideal model delta harmonic sigma weight residual 180.00 164.42 15.58 0 5.00e+00 4.00e-02 9.71e+00 ... (remaining 2813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 627 0.059 - 0.118: 104 0.118 - 0.178: 8 0.178 - 0.237: 1 0.237 - 0.296: 1 Chirality restraints: 741 Sorted by residual: chirality pdb=" CG LEU B 29 " pdb=" CB LEU B 29 " pdb=" CD1 LEU B 29 " pdb=" CD2 LEU B 29 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CB ILE A 149 " pdb=" CA ILE A 149 " pdb=" CG1 ILE A 149 " pdb=" CG2 ILE A 149 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" CA TYR A 86 " pdb=" N TYR A 86 " pdb=" C TYR A 86 " pdb=" CB TYR A 86 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 738 not shown) Planarity restraints: 820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 124 " -0.057 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO C 125 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 125 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 125 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 80 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.66e+00 pdb=" N PRO A 81 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 13 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO C 14 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " -0.029 5.00e-02 4.00e+02 ... (remaining 817 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 438 2.74 - 3.28: 4318 3.28 - 3.82: 7509 3.82 - 4.36: 8612 4.36 - 4.90: 15155 Nonbonded interactions: 36032 Sorted by model distance: nonbonded pdb=" NH1 ARG B 38 " pdb=" OD1 ASP B 89 " model vdw 2.205 3.120 nonbonded pdb=" O SER A 6 " pdb=" OG1 THR A 10 " model vdw 2.260 3.040 nonbonded pdb=" N GLN C 132 " pdb=" OE1 GLN C 132 " model vdw 2.289 3.120 nonbonded pdb=" N VAL C 35 " pdb=" OD1 ASN C 53 " model vdw 2.296 3.120 nonbonded pdb=" O THR B 174 " pdb=" OG1 THR B 174 " model vdw 2.301 3.040 ... (remaining 36027 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.020 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.530 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 0.004 0.062 4663 Z= 0.164 Angle : 0.681 9.980 6358 Z= 0.359 Chirality : 0.044 0.296 741 Planarity : 0.006 0.084 820 Dihedral : 14.748 84.325 1663 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.58 % Allowed : 24.76 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.34), residues: 611 helix: 2.60 (0.51), residues: 96 sheet: 1.93 (0.35), residues: 206 loop : 0.37 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.016 0.002 TYR A 86 PHE 0.009 0.001 PHE B 27 TRP 0.005 0.001 TRP B 47 HIS 0.006 0.002 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 4656) covalent geometry : angle 0.68072 / 0.36 ( 6344) SS BOND : bond 0.00357 / 0.24 ( 7) SS BOND : angle 0.69951 / 0.47 ( 14) hydrogen bonds : bond 0.11858 / 8.33 ( 203) hydrogen bonds : angle 6.09315 / 4.29 ( 627) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.177 Fit side-chains REVERT: A 147 GLU cc_start: 0.7759 (tt0) cc_final: 0.7204 (tt0) outliers start: 3 outliers final: 3 residues processed: 113 average time/residue: 0.0470 time to fit residues: 7.2965 Evaluate side-chains 110 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [54, 24, 48, 56, 26, 2, 16, 32, 31, 25, 58] chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 40 GLN C 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.133203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.114334 restraints weight = 6782.031| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.96 r_work: 0.3279 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4663 Z= 0.161 Angle : 0.597 9.163 6358 Z= 0.300 Chirality : 0.043 0.147 741 Planarity : 0.005 0.057 820 Dihedral : 4.891 41.266 659 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 6.63 % Allowed : 19.10 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.34), residues: 611 helix: 2.88 (0.51), residues: 96 sheet: 2.01 (0.35), residues: 215 loop : 0.38 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 38 TYR 0.021 0.002 TYR A 86 PHE 0.011 0.002 PHE A 148 TRP 0.006 0.001 TRP B 112 HIS 0.007 0.002 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 4656) covalent geometry : angle 0.59663 / 0.30 ( 6344) SS BOND : bond 0.00252 / 0.18 ( 7) SS BOND : angle 0.57057 / 0.39 ( 14) hydrogen bonds : bond 0.03455 / 2.37 ( 203) hydrogen bonds : angle 4.89171 / 3.47 ( 627) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.154 Fit side-chains REVERT: A 44 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7060 (mtt180) REVERT: A 90 MET cc_start: 0.7742 (mmt) cc_final: 0.7474 (mmt) REVERT: A 147 GLU cc_start: 0.7884 (tt0) cc_final: 0.7282 (tt0) REVERT: B 152 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7704 (mttt) REVERT: C 132 GLN cc_start: 0.8322 (mp10) cc_final: 0.7863 (mp10) REVERT: C 139 VAL cc_start: 0.8217 (t) cc_final: 0.7766 (p) outliers start: 34 outliers final: 21 residues processed: 133 average time/residue: 0.0459 time to fit residues: 8.5616 Evaluate side-chains 135 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 185 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [25, 40, 13, 5, 26, 54, 17, 31, 27, 42, 56] chunk 25 optimal weight: 0.0470 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 GLN C 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.132559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114405 restraints weight = 6796.150| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.79 r_work: 0.3261 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4663 Z= 0.132 Angle : 0.570 9.253 6358 Z= 0.285 Chirality : 0.042 0.142 741 Planarity : 0.005 0.057 820 Dihedral : 4.660 40.648 658 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 6.24 % Allowed : 18.71 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.34), residues: 611 helix: 2.90 (0.52), residues: 96 sheet: 2.08 (0.35), residues: 215 loop : 0.39 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.016 0.002 TYR A 86 PHE 0.009 0.001 PHE B 67 TRP 0.005 0.001 TRP B 112 HIS 0.007 0.002 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 4656) covalent geometry : angle 0.57039 / 0.29 ( 6344) SS BOND : bond 0.00328 / 0.25 ( 7) SS BOND : angle 0.47445 / 0.32 ( 14) hydrogen bonds : bond 0.03080 / 2.09 ( 203) hydrogen bonds : angle 4.62358 / 3.27 ( 627) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.144 Fit side-chains REVERT: A 90 MET cc_start: 0.7824 (mmt) cc_final: 0.7462 (mmt) REVERT: A 147 GLU cc_start: 0.7937 (tt0) cc_final: 0.7275 (tt0) REVERT: B 29 LEU cc_start: 0.8128 (tt) cc_final: 0.7880 (tt) REVERT: B 152 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7563 (mttt) REVERT: B 179 LEU cc_start: 0.7292 (tp) cc_final: 0.7072 (tp) REVERT: C 132 GLN cc_start: 0.8363 (mp10) cc_final: 0.7891 (mp10) REVERT: C 139 VAL cc_start: 0.8121 (t) cc_final: 0.7616 (m) outliers start: 32 outliers final: 23 residues processed: 121 average time/residue: 0.0414 time to fit residues: 7.1100 Evaluate side-chains 135 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 171 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [36, 44, 20, 33, 2, 17, 38, 41, 31, 27, 57] chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 0.0670 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 57 optimal weight: 0.0470 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.135615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.116969 restraints weight = 6770.086| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.94 r_work: 0.3269 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4663 Z= 0.129 Angle : 0.562 9.053 6358 Z= 0.283 Chirality : 0.042 0.142 741 Planarity : 0.005 0.057 820 Dihedral : 4.187 15.199 656 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 6.04 % Allowed : 19.10 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.34), residues: 611 helix: 2.93 (0.51), residues: 96 sheet: 2.05 (0.35), residues: 215 loop : 0.40 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 56 TYR 0.016 0.002 TYR A 86 PHE 0.008 0.001 PHE B 67 TRP 0.005 0.001 TRP C 154 HIS 0.005 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 4656) covalent geometry : angle 0.56237 / 0.28 ( 6344) SS BOND : bond 0.00326 / 0.23 ( 7) SS BOND : angle 0.38856 / 0.26 ( 14) hydrogen bonds : bond 0.02974 / 2.01 ( 203) hydrogen bonds : angle 4.59260 / 3.23 ( 627) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.164 Fit side-chains REVERT: A 44 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7007 (mtt180) REVERT: A 90 MET cc_start: 0.7850 (mmt) cc_final: 0.7518 (mmt) REVERT: A 147 GLU cc_start: 0.7961 (tt0) cc_final: 0.7332 (tt0) REVERT: B 152 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7663 (mttt) REVERT: C 109 LEU cc_start: 0.8052 (tp) cc_final: 0.7819 (tt) REVERT: C 132 GLN cc_start: 0.8413 (mp10) cc_final: 0.7908 (mp10) REVERT: C 139 VAL cc_start: 0.8187 (t) cc_final: 0.7684 (m) outliers start: 31 outliers final: 24 residues processed: 123 average time/residue: 0.0459 time to fit residues: 7.9069 Evaluate side-chains 136 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 185 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [4, 53, 30, 9, 25, 11, 54, 40, 3, 46, 33] chunk 4 optimal weight: 0.8980 chunk 53 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 HIS C 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.134512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.116406 restraints weight = 6732.081| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.79 r_work: 0.3314 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4663 Z= 0.134 Angle : 0.577 8.917 6358 Z= 0.284 Chirality : 0.042 0.141 741 Planarity : 0.005 0.056 820 Dihedral : 4.156 14.898 656 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 7.02 % Allowed : 18.52 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.34), residues: 611 helix: 2.69 (0.50), residues: 102 sheet: 2.09 (0.36), residues: 207 loop : 0.38 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 56 TYR 0.017 0.002 TYR A 86 PHE 0.008 0.001 PHE B 67 TRP 0.005 0.001 TRP C 154 HIS 0.005 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 4656) covalent geometry : angle 0.57726 / 0.28 ( 6344) SS BOND : bond 0.00252 / 0.17 ( 7) SS BOND : angle 0.43681 / 0.29 ( 14) hydrogen bonds : bond 0.02966 / 2.02 ( 203) hydrogen bonds : angle 4.51536 / 3.18 ( 627) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.189 Fit side-chains REVERT: A 44 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7033 (mtt180) REVERT: A 90 MET cc_start: 0.7821 (mmt) cc_final: 0.7479 (mmt) REVERT: A 147 GLU cc_start: 0.7900 (tt0) cc_final: 0.7276 (tt0) REVERT: B 152 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7720 (mttt) REVERT: B 165 SER cc_start: 0.8036 (OUTLIER) cc_final: 0.7498 (p) REVERT: C 132 GLN cc_start: 0.8438 (mp10) cc_final: 0.7919 (mp10) REVERT: C 139 VAL cc_start: 0.8225 (t) cc_final: 0.7732 (m) outliers start: 36 outliers final: 26 residues processed: 134 average time/residue: 0.0410 time to fit residues: 7.8804 Evaluate side-chains 144 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 185 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [39, 12, 52, 23, 47, 24, 13, 27, 53, 32, 38] chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114516 restraints weight = 6856.508| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.74 r_work: 0.3314 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4663 Z= 0.149 Angle : 0.597 10.223 6358 Z= 0.296 Chirality : 0.043 0.166 741 Planarity : 0.005 0.056 820 Dihedral : 4.202 14.844 656 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 7.21 % Allowed : 19.49 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.35), residues: 611 helix: 2.72 (0.50), residues: 101 sheet: 2.15 (0.37), residues: 207 loop : 0.38 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.018 0.002 TYR A 86 PHE 0.011 0.002 PHE C 64 TRP 0.007 0.001 TRP B 47 HIS 0.003 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 4656) covalent geometry : angle 0.59683 / 0.30 ( 6344) SS BOND : bond 0.00133 / 0.08 ( 7) SS BOND : angle 0.53045 / 0.36 ( 14) hydrogen bonds : bond 0.03052 / 2.06 ( 203) hydrogen bonds : angle 4.56658 / 3.21 ( 627) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.164 Fit side-chains REVERT: A 90 MET cc_start: 0.7829 (mmt) cc_final: 0.7474 (mmt) REVERT: A 147 GLU cc_start: 0.7936 (tt0) cc_final: 0.7182 (tt0) REVERT: B 152 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7681 (mttt) REVERT: B 165 SER cc_start: 0.8025 (OUTLIER) cc_final: 0.7482 (p) REVERT: C 132 GLN cc_start: 0.8435 (mp10) cc_final: 0.7918 (mp10) REVERT: C 139 VAL cc_start: 0.8216 (t) cc_final: 0.7727 (m) outliers start: 37 outliers final: 27 residues processed: 133 average time/residue: 0.0449 time to fit residues: 8.3324 Evaluate side-chains 145 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 185 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [27, 0, 5, 8, 43, 55, 35, 21, 9, 39, 13] chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.133008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114720 restraints weight = 6776.250| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.82 r_work: 0.3272 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4663 Z= 0.174 Angle : 0.612 9.945 6358 Z= 0.303 Chirality : 0.043 0.179 741 Planarity : 0.005 0.056 820 Dihedral : 4.297 15.079 656 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 7.60 % Allowed : 20.08 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.35), residues: 611 helix: 2.72 (0.51), residues: 101 sheet: 2.09 (0.37), residues: 209 loop : 0.36 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.020 0.002 TYR A 86 PHE 0.011 0.002 PHE C 64 TRP 0.008 0.001 TRP C 154 HIS 0.005 0.002 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 ( 4656) covalent geometry : angle 0.61217 / 0.30 ( 6344) SS BOND : bond 0.00259 / 0.19 ( 7) SS BOND : angle 0.57542 / 0.40 ( 14) hydrogen bonds : bond 0.03249 / 2.20 ( 203) hydrogen bonds : angle 4.64176 / 3.26 ( 627) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.165 Fit side-chains REVERT: A 90 MET cc_start: 0.7894 (mmt) cc_final: 0.7550 (mmt) REVERT: A 147 GLU cc_start: 0.7980 (tt0) cc_final: 0.7208 (tt0) REVERT: B 122 SER cc_start: 0.8379 (p) cc_final: 0.8152 (p) REVERT: B 152 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7725 (mttt) REVERT: B 165 SER cc_start: 0.8028 (OUTLIER) cc_final: 0.7607 (p) REVERT: C 109 LEU cc_start: 0.8115 (tp) cc_final: 0.7906 (tt) REVERT: C 132 GLN cc_start: 0.8458 (mp10) cc_final: 0.7947 (mp10) REVERT: C 139 VAL cc_start: 0.8224 (t) cc_final: 0.7735 (m) outliers start: 39 outliers final: 29 residues processed: 132 average time/residue: 0.0404 time to fit residues: 7.6878 Evaluate side-chains 142 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 201 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [31, 23, 11, 1, 35, 47, 21, 22, 18, 51, 16] chunk 31 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.0060 chunk 51 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.131796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113295 restraints weight = 6896.022| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.97 r_work: 0.3252 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4663 Z= 0.136 Angle : 0.595 9.934 6358 Z= 0.294 Chirality : 0.043 0.164 741 Planarity : 0.005 0.056 820 Dihedral : 4.230 15.242 656 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.85 % Allowed : 21.83 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.35), residues: 611 helix: 2.93 (0.52), residues: 95 sheet: 2.11 (0.37), residues: 209 loop : 0.39 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 38 TYR 0.017 0.002 TYR A 86 PHE 0.010 0.001 PHE C 64 TRP 0.007 0.001 TRP B 47 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 4656) covalent geometry : angle 0.59524 / 0.29 ( 6344) SS BOND : bond 0.00212 / 0.15 ( 7) SS BOND : angle 0.52326 / 0.36 ( 14) hydrogen bonds : bond 0.03045 / 2.07 ( 203) hydrogen bonds : angle 4.57206 / 3.20 ( 627) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.160 Fit side-chains REVERT: A 90 MET cc_start: 0.7861 (mmt) cc_final: 0.7493 (mmt) REVERT: A 147 GLU cc_start: 0.8041 (tt0) cc_final: 0.7248 (tt0) REVERT: B 122 SER cc_start: 0.8391 (p) cc_final: 0.8166 (p) REVERT: B 152 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7660 (mttt) REVERT: B 165 SER cc_start: 0.8003 (OUTLIER) cc_final: 0.7473 (p) REVERT: C 132 GLN cc_start: 0.8470 (mp10) cc_final: 0.7919 (mp10) REVERT: C 139 VAL cc_start: 0.8175 (t) cc_final: 0.7694 (m) outliers start: 30 outliers final: 26 residues processed: 114 average time/residue: 0.0390 time to fit residues: 6.3442 Evaluate side-chains 126 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 201 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [11, 53, 18, 56, 42, 15, 25, 51, 17, 34, 13] chunk 11 optimal weight: 0.0980 chunk 53 optimal weight: 0.0870 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 17 optimal weight: 0.0270 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.132214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114837 restraints weight = 6808.040| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.72 r_work: 0.3289 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4663 Z= 0.104 Angle : 0.578 9.895 6358 Z= 0.285 Chirality : 0.042 0.141 741 Planarity : 0.005 0.055 820 Dihedral : 4.088 15.165 656 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.48 % Allowed : 23.78 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.35), residues: 611 helix: 2.68 (0.51), residues: 101 sheet: 2.03 (0.36), residues: 213 loop : 0.45 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 56 TYR 0.013 0.001 TYR A 86 PHE 0.007 0.001 PHE C 64 TRP 0.006 0.001 TRP B 47 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 ( 4656) covalent geometry : angle 0.57844 / 0.29 ( 6344) SS BOND : bond 0.00194 / 0.14 ( 7) SS BOND : angle 0.47353 / 0.34 ( 14) hydrogen bonds : bond 0.02753 / 1.87 ( 203) hydrogen bonds : angle 4.44077 / 3.11 ( 627) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.159 Fit side-chains REVERT: A 90 MET cc_start: 0.7797 (mmt) cc_final: 0.7414 (mmt) REVERT: A 147 GLU cc_start: 0.8035 (tt0) cc_final: 0.7202 (tt0) REVERT: B 122 SER cc_start: 0.8345 (p) cc_final: 0.8127 (p) REVERT: B 152 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7543 (mttt) REVERT: C 132 GLN cc_start: 0.8448 (mp10) cc_final: 0.7914 (mp10) REVERT: C 139 VAL cc_start: 0.8058 (t) cc_final: 0.7580 (m) outliers start: 23 outliers final: 20 residues processed: 121 average time/residue: 0.0422 time to fit residues: 7.3403 Evaluate side-chains 121 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [14, 58, 30, 11, 45, 47, 0, 38, 44, 37, 39] chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.131498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113189 restraints weight = 6732.847| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.89 r_work: 0.3265 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4663 Z= 0.240 Angle : 0.669 9.978 6358 Z= 0.338 Chirality : 0.046 0.240 741 Planarity : 0.005 0.058 820 Dihedral : 4.551 16.584 656 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.68 % Allowed : 23.78 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.35), residues: 611 helix: 2.52 (0.52), residues: 103 sheet: 2.08 (0.37), residues: 209 loop : 0.22 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.026 0.002 TYR A 86 PHE 0.014 0.002 PHE C 64 TRP 0.012 0.002 TRP C 154 HIS 0.006 0.002 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.24 ( 4656) covalent geometry : angle 0.66867 / 0.34 ( 6344) SS BOND : bond 0.00291 / 0.21 ( 7) SS BOND : angle 0.71664 / 0.47 ( 14) hydrogen bonds : bond 0.03745 / 2.52 ( 203) hydrogen bonds : angle 4.83357 / 3.38 ( 627) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.163 Fit side-chains REVERT: A 90 MET cc_start: 0.7885 (mmt) cc_final: 0.7534 (mmt) REVERT: A 147 GLU cc_start: 0.7979 (tt0) cc_final: 0.7211 (tt0) REVERT: B 152 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7718 (mttt) REVERT: C 114 GLN cc_start: 0.7447 (mt0) cc_final: 0.7034 (mt0) REVERT: C 132 GLN cc_start: 0.8476 (mp10) cc_final: 0.7961 (mp10) REVERT: C 139 VAL cc_start: 0.8246 (t) cc_final: 0.7847 (p) outliers start: 24 outliers final: 19 residues processed: 118 average time/residue: 0.0367 time to fit residues: 6.2595 Evaluate side-chains 126 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [54, 52, 41, 10, 30, 48, 46, 0, 17, 2, 35] chunk 54 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.133424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114969 restraints weight = 6803.611| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.94 r_work: 0.3279 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4663 Z= 0.156 Angle : 0.618 9.875 6358 Z= 0.309 Chirality : 0.043 0.155 741 Planarity : 0.005 0.056 820 Dihedral : 4.407 16.298 656 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.48 % Allowed : 23.39 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.35), residues: 611 helix: 2.89 (0.53), residues: 96 sheet: 1.95 (0.37), residues: 215 loop : 0.28 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.019 0.002 TYR A 86 PHE 0.010 0.002 PHE C 64 TRP 0.007 0.001 TRP C 154 HIS 0.005 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 4656) covalent geometry : angle 0.61818 / 0.31 ( 6344) SS BOND : bond 0.00225 / 0.16 ( 7) SS BOND : angle 0.59146 / 0.40 ( 14) hydrogen bonds : bond 0.03259 / 2.20 ( 203) hydrogen bonds : angle 4.65657 / 3.26 ( 627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1050.30 seconds wall clock time: 18 minutes 47.82 seconds (1127.82 seconds total)