Starting phenix.real_space_refine on Tue Mar 3 14:11:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7til_25913/03_2026/7til_25913.cif Found real_map, /net/cci-nas-00/data/ceres_data/7til_25913/03_2026/7til_25913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7til_25913/03_2026/7til_25913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7til_25913/03_2026/7til_25913.map" model { file = "/net/cci-nas-00/data/ceres_data/7til_25913/03_2026/7til_25913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7til_25913/03_2026/7til_25913.cif" } resolution = 3.7 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= -0.000 sd= 0.005 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 12 5.16 5 C 3707 2.51 5 N 1037 2.21 5 O 1059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5815 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2876 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 341} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 2939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2939 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 349} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 1.29, per 1000 atoms: 0.22 Number of scatterers: 5815 At special positions: 0 Unit cell: (65.65, 107.25, 112.45, 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 12 16.00 O 1059 8.00 N 1037 7.00 C 3707 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: 0.43 Conformation dependent library (CDL) restraints added in 338.1 milliseconds 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 4 sheets defined 55.6% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 removed outlier: 3.616A pdb=" N GLN A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 26 Processing helix chain 'A' and resid 27 through 31 removed outlier: 3.847A pdb=" N TRP A 31 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 48 Processing helix chain 'A' and resid 48 through 59 removed outlier: 3.676A pdb=" N VAL A 52 " --> pdb=" O ASN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 100 Processing helix chain 'A' and resid 101 through 118 removed outlier: 3.516A pdb=" N GLN A 117 " --> pdb=" O TYR A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 129 through 136 removed outlier: 4.328A pdb=" N TRP A 133 " --> pdb=" O GLN A 129 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 150 Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.625A pdb=" N ALA A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 189 removed outlier: 3.561A pdb=" N ARG A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 removed outlier: 3.994A pdb=" N GLU A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 202 Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 273 through 277 removed outlier: 3.639A pdb=" N ALA A 277 " --> pdb=" O HIS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 307 Processing helix chain 'A' and resid 316 through 323 Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.970A pdb=" N VAL A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.593A pdb=" N TYR A 366 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 380 removed outlier: 3.626A pdb=" N VAL A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 16 removed outlier: 3.582A pdb=" N GLN B 16 " --> pdb=" O ALA B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 26 Processing helix chain 'B' and resid 41 through 48 Processing helix chain 'B' and resid 48 through 61 removed outlier: 4.028A pdb=" N VAL B 52 " --> pdb=" O ASN B 48 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 100 removed outlier: 3.615A pdb=" N ASP B 100 " --> pdb=" O ILE B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 118 removed outlier: 3.552A pdb=" N GLU B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 129 through 135 removed outlier: 4.273A pdb=" N TRP B 133 " --> pdb=" O GLN B 129 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.567A pdb=" N GLN B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 165 removed outlier: 3.727A pdb=" N LEU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 160 through 165' Processing helix chain 'B' and resid 177 through 189 removed outlier: 3.567A pdb=" N GLU B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 188 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 197 removed outlier: 3.828A pdb=" N GLU B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 202 Processing helix chain 'B' and resid 230 through 235 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 293 through 307 Processing helix chain 'B' and resid 316 through 323 removed outlier: 3.551A pdb=" N PHE B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 357 removed outlier: 3.565A pdb=" N VAL B 356 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 381 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 36 removed outlier: 3.578A pdb=" N GLN A 33 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 89 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 66 " --> pdb=" O HIS A 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 230 removed outlier: 3.595A pdb=" N VAL A 214 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 244 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N TRP A 289 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL A 246 " --> pdb=" O TRP A 289 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE A 286 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 33 through 36 removed outlier: 3.597A pdb=" N GLN B 33 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG B 86 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 229 removed outlier: 6.829A pdb=" N ARG B 243 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL B 266 " --> pdb=" O ARG B 243 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU B 245 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE B 286 " --> pdb=" O GLU B 311 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 708 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: 0.85 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1956 1.34 - 1.46: 1205 1.46 - 1.58: 2774 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 5955 Sorted by residual: bond pdb=" CA PRO A 32 " pdb=" CB PRO A 32 " ideal model delta sigma weight residual 1.533 1.517 0.016 1.80e-02 3.09e+03 7.61e-01 bond pdb=" C ASP B 101 " pdb=" O ASP B 101 " ideal model delta sigma weight residual 1.248 1.238 0.011 1.26e-02 6.30e+03 7.28e-01 bond pdb=" CA ASP B 262 " pdb=" CB ASP B 262 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.47e-01 bond pdb=" CB LYS B 334 " pdb=" CG LYS B 334 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.77e-01 bond pdb=" C ILE B 37 " pdb=" N GLY B 38 " ideal model delta sigma weight residual 1.322 1.331 -0.009 1.20e-02 6.94e+03 5.61e-01 ... (remaining 5950 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 7961 1.75 - 3.51: 146 3.51 - 5.26: 8 5.26 - 7.01: 3 7.01 - 8.77: 1 Bond angle restraints: 8119 Sorted by residual: angle pdb=" C PRO B 261 " pdb=" N ASP B 262 " pdb=" CA ASP B 262 " ideal model delta sigma weight residual 121.54 127.04 -5.50 1.91e+00 2.74e-01 8.29e+00 angle pdb=" CA LYS B 172 " pdb=" CB LYS B 172 " pdb=" CG LYS B 172 " ideal model delta sigma weight residual 114.10 119.61 -5.51 2.00e+00 2.50e-01 7.58e+00 angle pdb=" CA LYS A 172 " pdb=" CB LYS A 172 " pdb=" CG LYS A 172 " ideal model delta sigma weight residual 114.10 119.55 -5.45 2.00e+00 2.50e-01 7.43e+00 angle pdb=" N LYS A 172 " pdb=" CA LYS A 172 " pdb=" C LYS A 172 " ideal model delta sigma weight residual 113.19 109.39 3.80 1.58e+00 4.01e-01 5.79e+00 angle pdb=" CA LYS A 172 " pdb=" C LYS A 172 " pdb=" O LYS A 172 " ideal model delta sigma weight residual 119.08 121.36 -2.28 1.03e+00 9.43e-01 4.91e+00 ... (remaining 8114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3223 17.53 - 35.06: 289 35.06 - 52.58: 54 52.58 - 70.11: 9 70.11 - 87.64: 6 Dihedral angle restraints: 3581 sinusoidal: 1435 harmonic: 2146 Sorted by residual: dihedral pdb=" CA GLU A 57 " pdb=" C GLU A 57 " pdb=" N ASN A 58 " pdb=" CA ASN A 58 " ideal model delta harmonic sigma weight residual 180.00 159.33 20.67 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ARG B 359 " pdb=" C ARG B 359 " pdb=" N GLY B 360 " pdb=" CA GLY B 360 " ideal model delta harmonic sigma weight residual 180.00 163.77 16.23 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CG ARG B 86 " pdb=" CD ARG B 86 " pdb=" NE ARG B 86 " pdb=" CZ ARG B 86 " ideal model delta sinusoidal sigma weight residual 90.00 130.55 -40.55 2 1.50e+01 4.44e-03 9.02e+00 ... (remaining 3578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 654 0.033 - 0.066: 199 0.066 - 0.099: 49 0.099 - 0.132: 11 0.132 - 0.165: 2 Chirality restraints: 915 Sorted by residual: chirality pdb=" CA GLU A 57 " pdb=" N GLU A 57 " pdb=" C GLU A 57 " pdb=" CB GLU A 57 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA ASP B 262 " pdb=" N ASP B 262 " pdb=" C ASP B 262 " pdb=" CB ASP B 262 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 912 not shown) Planarity restraints: 1049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 27 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO B 28 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 28 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 28 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 3 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO B 4 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 4 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 4 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 53 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C LEU A 53 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU A 53 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG A 54 " 0.008 2.00e-02 2.50e+03 ... (remaining 1046 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1214 2.78 - 3.31: 5637 3.31 - 3.84: 9424 3.84 - 4.37: 10546 4.37 - 4.90: 18185 Nonbonded interactions: 45006 Sorted by model distance: nonbonded pdb=" O GLU B 318 " pdb=" NE2 GLN B 322 " model vdw 2.253 3.120 nonbonded pdb=" OE1 GLU B 331 " pdb=" NZ LYS B 334 " model vdw 2.258 3.120 nonbonded pdb=" OD2 ASP A 186 " pdb=" OG SER A 194 " model vdw 2.261 3.040 nonbonded pdb=" O GLU B 233 " pdb=" OG1 THR B 237 " model vdw 2.267 3.040 nonbonded pdb=" OD2 ASP B 186 " pdb=" OG SER B 194 " model vdw 2.284 3.040 ... (remaining 45001 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 'B' and (resid 1 through 325 or resid 335 through 381)) } 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: 6.680 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: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.840 Find NCS groups from input model: 0.090 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 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 : 0.002 0.035 5955 Z= 0.105 Angle : 0.536 8.768 8119 Z= 0.280 Chirality : 0.035 0.165 915 Planarity : 0.004 0.040 1049 Dihedral : 13.783 87.638 2181 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.31), residues: 729 helix: 1.50 (0.30), residues: 342 sheet: -0.39 (0.62), residues: 65 loop : -1.38 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 130 TYR 0.005 0.001 TYR B 288 PHE 0.009 0.001 PHE B 205 TRP 0.010 0.001 TRP B 289 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 5955) covalent geometry : angle 0.53595 ( 8119) hydrogen bonds : bond 0.22853 ( 247) hydrogen bonds : angle 6.66390 ( 708) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9104 (mm) cc_final: 0.8739 (mm) REVERT: A 205 PHE cc_start: 0.6997 (m-80) cc_final: 0.6681 (m-10) REVERT: B 85 MET cc_start: 0.7782 (ppp) cc_final: 0.7171 (ppp) REVERT: B 249 ASN cc_start: 0.7516 (t0) cc_final: 0.6902 (t0) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1101 time to fit residues: 19.1137 Evaluate side-chains 72 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN B 322 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.078114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.057106 restraints weight = 23446.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.058958 restraints weight = 13779.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.060171 restraints weight = 9987.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.060989 restraints weight = 8157.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.061458 restraints weight = 7164.911| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5955 Z= 0.152 Angle : 0.668 12.657 8119 Z= 0.326 Chirality : 0.041 0.171 915 Planarity : 0.005 0.045 1049 Dihedral : 3.927 19.745 798 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.15 % Allowed : 11.86 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.32), residues: 729 helix: 1.17 (0.29), residues: 359 sheet: -0.32 (0.61), residues: 66 loop : -1.12 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 54 TYR 0.018 0.003 TYR A 353 PHE 0.018 0.002 PHE B 350 TRP 0.012 0.001 TRP B 289 HIS 0.004 0.001 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5955) covalent geometry : angle 0.66761 ( 8119) hydrogen bonds : bond 0.04318 ( 247) hydrogen bonds : angle 4.83373 ( 708) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.9146 (mp0) cc_final: 0.8776 (tp30) REVERT: B 66 LYS cc_start: 0.9187 (tmtt) cc_final: 0.8953 (tmtt) REVERT: B 85 MET cc_start: 0.7995 (ppp) cc_final: 0.7719 (ppp) REVERT: B 86 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7899 (mpp80) REVERT: B 249 ASN cc_start: 0.7497 (t0) cc_final: 0.6751 (t0) outliers start: 7 outliers final: 4 residues processed: 88 average time/residue: 0.0931 time to fit residues: 10.5204 Evaluate side-chains 75 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 271 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 43 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A 274 HIS A 306 HIS ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.075388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.054062 restraints weight = 23590.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.055741 restraints weight = 14531.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.056861 restraints weight = 10801.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.057612 restraints weight = 8944.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.058059 restraints weight = 7936.532| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5955 Z= 0.177 Angle : 0.655 13.621 8119 Z= 0.317 Chirality : 0.040 0.156 915 Planarity : 0.004 0.037 1049 Dihedral : 4.004 19.844 798 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.81 % Allowed : 14.50 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.32), residues: 729 helix: 1.18 (0.29), residues: 355 sheet: -0.57 (0.60), residues: 66 loop : -1.11 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 103 TYR 0.010 0.002 TYR B 108 PHE 0.015 0.002 PHE A 173 TRP 0.023 0.002 TRP B 289 HIS 0.003 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 5955) covalent geometry : angle 0.65510 ( 8119) hydrogen bonds : bond 0.04018 ( 247) hydrogen bonds : angle 4.58901 ( 708) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 366 TYR cc_start: 0.7729 (m-80) cc_final: 0.7027 (m-80) REVERT: B 172 LYS cc_start: 0.8095 (mmtp) cc_final: 0.7651 (mmmt) REVERT: B 249 ASN cc_start: 0.7678 (t0) cc_final: 0.6955 (t0) outliers start: 11 outliers final: 9 residues processed: 82 average time/residue: 0.0820 time to fit residues: 8.8846 Evaluate side-chains 74 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 167 HIS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 274 HIS ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** 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 = 0.3641 r_free = 0.3641 target = 0.076058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.054231 restraints weight = 23301.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.056029 restraints weight = 13766.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.057256 restraints weight = 10002.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.058048 restraints weight = 8151.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.058504 restraints weight = 7153.320| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5955 Z= 0.159 Angle : 0.649 12.538 8119 Z= 0.310 Chirality : 0.039 0.166 915 Planarity : 0.004 0.055 1049 Dihedral : 3.991 19.444 798 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.98 % Allowed : 15.65 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.32), residues: 729 helix: 1.02 (0.29), residues: 359 sheet: -0.33 (0.63), residues: 66 loop : -1.12 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 103 TYR 0.011 0.002 TYR B 108 PHE 0.013 0.002 PHE B 224 TRP 0.023 0.001 TRP B 289 HIS 0.008 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 5955) covalent geometry : angle 0.64935 ( 8119) hydrogen bonds : bond 0.03556 ( 247) hydrogen bonds : angle 4.41794 ( 708) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8634 (tptp) cc_final: 0.8364 (tptp) REVERT: A 57 GLU cc_start: 0.8995 (pt0) cc_final: 0.8615 (tp30) REVERT: B 172 LYS cc_start: 0.8138 (mmtp) cc_final: 0.7662 (mmmt) REVERT: B 249 ASN cc_start: 0.7587 (t0) cc_final: 0.6803 (t0) REVERT: B 289 TRP cc_start: 0.8376 (t60) cc_final: 0.7529 (t60) REVERT: B 318 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8781 (pm20) outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 0.0816 time to fit residues: 8.2915 Evaluate side-chains 70 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 69 optimal weight: 0.0570 chunk 17 optimal weight: 0.6980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.073861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.052248 restraints weight = 23797.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.053941 restraints weight = 14246.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.055048 restraints weight = 10432.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.055818 restraints weight = 8573.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.056308 restraints weight = 7542.356| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5955 Z= 0.111 Angle : 0.613 11.055 8119 Z= 0.292 Chirality : 0.038 0.180 915 Planarity : 0.004 0.031 1049 Dihedral : 3.833 19.111 798 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.65 % Allowed : 16.64 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.32), residues: 729 helix: 1.16 (0.29), residues: 360 sheet: -0.28 (0.63), residues: 66 loop : -1.09 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 86 TYR 0.013 0.002 TYR B 108 PHE 0.016 0.001 PHE B 224 TRP 0.018 0.001 TRP B 289 HIS 0.005 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 5955) covalent geometry : angle 0.61331 ( 8119) hydrogen bonds : bond 0.03194 ( 247) hydrogen bonds : angle 4.19318 ( 708) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 315 MET cc_start: 0.7602 (mmt) cc_final: 0.7138 (mmm) REVERT: B 172 LYS cc_start: 0.8224 (mmtp) cc_final: 0.7701 (mmmt) REVERT: B 249 ASN cc_start: 0.7487 (t0) cc_final: 0.6623 (t0) REVERT: B 289 TRP cc_start: 0.8401 (t60) cc_final: 0.7733 (t60) REVERT: B 315 MET cc_start: 0.8043 (mmm) cc_final: 0.7837 (mmt) REVERT: B 318 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8781 (pm20) outliers start: 10 outliers final: 7 residues processed: 73 average time/residue: 0.0721 time to fit residues: 7.2625 Evaluate side-chains 70 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 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 = 0.3573 r_free = 0.3573 target = 0.073296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.051509 restraints weight = 24162.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.053227 restraints weight = 14450.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.054379 restraints weight = 10605.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.055135 restraints weight = 8720.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.055588 restraints weight = 7692.390| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5955 Z= 0.142 Angle : 0.626 10.467 8119 Z= 0.299 Chirality : 0.039 0.161 915 Planarity : 0.004 0.032 1049 Dihedral : 3.841 18.821 798 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.65 % Allowed : 16.64 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.32), residues: 729 helix: 1.16 (0.29), residues: 360 sheet: -0.30 (0.62), residues: 66 loop : -1.03 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 86 TYR 0.013 0.002 TYR B 108 PHE 0.017 0.002 PHE B 224 TRP 0.020 0.001 TRP B 289 HIS 0.002 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 5955) covalent geometry : angle 0.62618 ( 8119) hydrogen bonds : bond 0.03323 ( 247) hydrogen bonds : angle 4.16829 ( 708) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.7658 (mmt) cc_final: 0.7208 (mmm) REVERT: B 172 LYS cc_start: 0.8241 (mmtp) cc_final: 0.7717 (mmmt) REVERT: B 249 ASN cc_start: 0.7568 (t0) cc_final: 0.6819 (t0) REVERT: B 318 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8740 (pm20) outliers start: 10 outliers final: 6 residues processed: 73 average time/residue: 0.0867 time to fit residues: 8.3340 Evaluate side-chains 69 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 60 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 chunk 55 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 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 = 0.3589 r_free = 0.3589 target = 0.074119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.052239 restraints weight = 24090.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.054006 restraints weight = 14318.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.055199 restraints weight = 10467.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.055973 restraints weight = 8601.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.056478 restraints weight = 7576.077| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5955 Z= 0.110 Angle : 0.621 11.101 8119 Z= 0.295 Chirality : 0.038 0.194 915 Planarity : 0.004 0.031 1049 Dihedral : 3.741 18.762 798 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.48 % Allowed : 18.29 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.33), residues: 729 helix: 1.26 (0.29), residues: 360 sheet: -0.23 (0.62), residues: 66 loop : -1.05 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 86 TYR 0.013 0.002 TYR B 108 PHE 0.018 0.001 PHE B 224 TRP 0.010 0.001 TRP A 289 HIS 0.003 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 5955) covalent geometry : angle 0.62088 ( 8119) hydrogen bonds : bond 0.03065 ( 247) hydrogen bonds : angle 4.07444 ( 708) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.7614 (mmt) cc_final: 0.7210 (mmm) REVERT: B 172 LYS cc_start: 0.8205 (mmtp) cc_final: 0.7672 (mmmt) REVERT: B 249 ASN cc_start: 0.7503 (t0) cc_final: 0.6700 (t0) REVERT: B 289 TRP cc_start: 0.8826 (t60) cc_final: 0.8446 (t60) outliers start: 9 outliers final: 8 residues processed: 77 average time/residue: 0.0946 time to fit residues: 9.3878 Evaluate side-chains 72 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 51 optimal weight: 0.0040 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 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 = 0.3594 r_free = 0.3594 target = 0.074339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.052766 restraints weight = 23746.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.054524 restraints weight = 14149.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.055677 restraints weight = 10323.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.056502 restraints weight = 8472.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.056923 restraints weight = 7429.615| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5955 Z= 0.105 Angle : 0.623 10.834 8119 Z= 0.295 Chirality : 0.039 0.202 915 Planarity : 0.004 0.031 1049 Dihedral : 3.659 18.764 798 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.48 % Allowed : 18.45 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.32), residues: 729 helix: 1.32 (0.29), residues: 359 sheet: -0.21 (0.61), residues: 66 loop : -1.03 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 86 TYR 0.014 0.001 TYR B 108 PHE 0.018 0.001 PHE B 224 TRP 0.010 0.001 TRP A 289 HIS 0.003 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 5955) covalent geometry : angle 0.62340 ( 8119) hydrogen bonds : bond 0.03018 ( 247) hydrogen bonds : angle 4.03536 ( 708) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 315 MET cc_start: 0.7649 (mmt) cc_final: 0.7249 (mmm) REVERT: B 85 MET cc_start: 0.7968 (ppp) cc_final: 0.7502 (ppp) REVERT: B 172 LYS cc_start: 0.8205 (mmtp) cc_final: 0.7666 (mmmt) REVERT: B 249 ASN cc_start: 0.7556 (t0) cc_final: 0.6721 (t0) REVERT: B 289 TRP cc_start: 0.8793 (t60) cc_final: 0.8365 (t60) outliers start: 9 outliers final: 8 residues processed: 74 average time/residue: 0.0933 time to fit residues: 8.9768 Evaluate side-chains 70 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 28 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 40 optimal weight: 0.0010 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 60 optimal weight: 0.0050 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 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 = 0.3600 r_free = 0.3600 target = 0.074629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.053036 restraints weight = 24061.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.054811 restraints weight = 14251.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.056017 restraints weight = 10377.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.056825 restraints weight = 8474.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.057286 restraints weight = 7421.996| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5955 Z= 0.104 Angle : 0.660 15.699 8119 Z= 0.303 Chirality : 0.039 0.221 915 Planarity : 0.004 0.031 1049 Dihedral : 3.616 18.642 798 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.32 % Allowed : 19.44 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.32), residues: 729 helix: 1.36 (0.29), residues: 359 sheet: -0.19 (0.61), residues: 66 loop : -1.02 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 86 TYR 0.014 0.001 TYR B 108 PHE 0.019 0.001 PHE B 224 TRP 0.008 0.001 TRP A 95 HIS 0.003 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 5955) covalent geometry : angle 0.66009 ( 8119) hydrogen bonds : bond 0.02944 ( 247) hydrogen bonds : angle 3.99883 ( 708) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8526 (tptp) cc_final: 0.8271 (tptp) REVERT: A 53 LEU cc_start: 0.9677 (mt) cc_final: 0.9327 (pp) REVERT: A 299 MET cc_start: 0.8291 (mtp) cc_final: 0.8010 (mtm) REVERT: A 315 MET cc_start: 0.7697 (mmt) cc_final: 0.7289 (mmm) REVERT: B 172 LYS cc_start: 0.8197 (mmtp) cc_final: 0.7650 (mmmt) REVERT: B 249 ASN cc_start: 0.7596 (t0) cc_final: 0.6729 (t0) REVERT: B 289 TRP cc_start: 0.8651 (t60) cc_final: 0.8124 (t60) outliers start: 8 outliers final: 8 residues processed: 74 average time/residue: 0.0883 time to fit residues: 8.4066 Evaluate side-chains 74 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 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 = 0.3582 r_free = 0.3582 target = 0.074069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.051525 restraints weight = 24171.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.053291 restraints weight = 14418.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.054474 restraints weight = 10577.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.055198 restraints weight = 8699.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.055753 restraints weight = 7699.021| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5955 Z= 0.133 Angle : 0.688 14.003 8119 Z= 0.317 Chirality : 0.040 0.231 915 Planarity : 0.004 0.032 1049 Dihedral : 3.711 19.059 798 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.32 % Allowed : 19.60 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.33), residues: 729 helix: 1.34 (0.29), residues: 358 sheet: -0.20 (0.62), residues: 66 loop : -0.99 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 86 TYR 0.013 0.002 TYR B 108 PHE 0.018 0.002 PHE B 224 TRP 0.010 0.001 TRP A 289 HIS 0.004 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 5955) covalent geometry : angle 0.68791 ( 8119) hydrogen bonds : bond 0.03156 ( 247) hydrogen bonds : angle 4.05219 ( 708) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8553 (tptp) cc_final: 0.8297 (tptp) REVERT: A 299 MET cc_start: 0.8354 (mtp) cc_final: 0.8080 (mtm) REVERT: A 315 MET cc_start: 0.7714 (mmt) cc_final: 0.7463 (mmm) REVERT: B 85 MET cc_start: 0.7981 (ppp) cc_final: 0.7515 (ppp) REVERT: B 172 LYS cc_start: 0.8264 (mmtp) cc_final: 0.7715 (mmmt) REVERT: B 225 LYS cc_start: 0.9340 (tptt) cc_final: 0.9139 (tptm) REVERT: B 249 ASN cc_start: 0.7592 (t0) cc_final: 0.6814 (t0) REVERT: B 289 TRP cc_start: 0.8718 (t60) cc_final: 0.8370 (t60) outliers start: 8 outliers final: 7 residues processed: 70 average time/residue: 0.0821 time to fit residues: 7.5264 Evaluate side-chains 70 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 chunk 64 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.074146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.052517 restraints weight = 23765.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.054240 restraints weight = 14263.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.055410 restraints weight = 10468.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.056168 restraints weight = 8598.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.056678 restraints weight = 7579.593| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5955 Z= 0.114 Angle : 0.671 13.137 8119 Z= 0.308 Chirality : 0.039 0.235 915 Planarity : 0.004 0.042 1049 Dihedral : 3.674 18.782 798 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.32 % Allowed : 20.43 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.33), residues: 729 helix: 1.32 (0.29), residues: 358 sheet: -0.13 (0.63), residues: 66 loop : -1.00 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 86 TYR 0.014 0.001 TYR B 108 PHE 0.018 0.001 PHE B 224 TRP 0.008 0.001 TRP A 289 HIS 0.003 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5955) covalent geometry : angle 0.67051 ( 8119) hydrogen bonds : bond 0.03033 ( 247) hydrogen bonds : angle 4.01536 ( 708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1348.62 seconds wall clock time: 23 minutes 50.68 seconds (1430.68 seconds total)