Starting phenix.real_space_refine on Tue Feb 11 13:54:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7til_25913/02_2025/7til_25913.cif Found real_map, /net/cci-nas-00/data/ceres_data/7til_25913/02_2025/7til_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_25913/02_2025/7til_25913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7til_25913/02_2025/7til_25913.map" model { file = "/net/cci-nas-00/data/ceres_data/7til_25913/02_2025/7til_25913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7til_25913/02_2025/7til_25913.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP: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: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 5.60, per 1000 atoms: 0.96 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: 1.50 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.73 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: 1.56 Time building geometry restraints manager: 1.73 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: 10.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.160 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.720 ------------------------------------------------------------------------------- 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= 0.151 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 : 8.12 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (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 TRP 0.010 0.001 TRP B 289 HIS 0.002 0.000 HIS A 280 PHE 0.009 0.001 PHE B 205 TYR 0.005 0.001 TYR B 288 ARG 0.006 0.000 ARG A 130 *********************** 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 : 0.660 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: 0.7262 (ppp) REVERT: B 249 ASN cc_start: 0.7516 (t0) cc_final: 0.6903 (t0) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2921 time to fit residues: 49.8308 Evaluate side-chains 73 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.2980 chunk 55 optimal weight: 0.2980 chunk 30 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 42 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.079141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.057825 restraints weight = 23202.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.059793 restraints weight = 13332.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.061089 restraints weight = 9561.284| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2770 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= 0.183 Angle : 0.657 13.429 8119 Z= 0.321 Chirality : 0.040 0.163 915 Planarity : 0.005 0.064 1049 Dihedral : 3.783 19.738 798 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.66 % Allowed : 11.20 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.32), residues: 729 helix: 1.18 (0.29), residues: 359 sheet: -0.29 (0.61), residues: 66 loop : -1.13 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 289 HIS 0.004 0.001 HIS A 55 PHE 0.018 0.002 PHE B 350 TYR 0.019 0.003 TYR B 351 ARG 0.008 0.001 ARG B 86 *********************** 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 88 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.9241 (mp0) cc_final: 0.8822 (tp30) REVERT: A 205 PHE cc_start: 0.7386 (m-80) cc_final: 0.7166 (m-10) REVERT: A 374 LEU cc_start: 0.9468 (mt) cc_final: 0.9267 (pp) REVERT: B 249 ASN cc_start: 0.7407 (t0) cc_final: 0.6627 (t0) outliers start: 4 outliers final: 2 residues processed: 86 average time/residue: 0.2106 time to fit residues: 23.3565 Evaluate side-chains 71 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL 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 64 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.075407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.054099 restraints weight = 23757.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.055826 restraints weight = 14392.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.056958 restraints weight = 10594.682| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5955 Z= 0.287 Angle : 0.659 9.600 8119 Z= 0.326 Chirality : 0.040 0.178 915 Planarity : 0.005 0.039 1049 Dihedral : 4.077 19.814 798 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.98 % Allowed : 13.34 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.31), residues: 729 helix: 1.16 (0.29), residues: 355 sheet: -0.66 (0.58), residues: 66 loop : -1.07 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 289 HIS 0.003 0.001 HIS A 280 PHE 0.013 0.002 PHE B 224 TYR 0.010 0.002 TYR B 108 ARG 0.005 0.001 ARG B 103 *********************** 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 88 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 366 TYR cc_start: 0.7771 (m-80) cc_final: 0.7072 (m-80) REVERT: B 172 LYS cc_start: 0.8183 (mmtp) cc_final: 0.7718 (mmmt) REVERT: B 249 ASN cc_start: 0.7717 (t0) cc_final: 0.7028 (t0) outliers start: 12 outliers final: 9 residues processed: 82 average time/residue: 0.1854 time to fit residues: 20.0824 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 : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS 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 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 36 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 1 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 0.0020 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 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 = 0.3653 r_free = 0.3653 target = 0.076513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.055139 restraints weight = 23873.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.056930 restraints weight = 14287.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.058128 restraints weight = 10502.514| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5955 Z= 0.159 Angle : 0.636 13.219 8119 Z= 0.301 Chirality : 0.039 0.177 915 Planarity : 0.004 0.032 1049 Dihedral : 3.878 19.236 798 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.32 % Allowed : 14.66 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.32), residues: 729 helix: 1.23 (0.29), residues: 355 sheet: -0.53 (0.59), residues: 66 loop : -1.05 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 289 HIS 0.002 0.001 HIS A 55 PHE 0.015 0.001 PHE B 224 TYR 0.013 0.002 TYR B 108 ARG 0.005 0.000 ARG B 86 *********************** 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 80 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8961 (pt0) cc_final: 0.8474 (tp30) REVERT: B 172 LYS cc_start: 0.8110 (mmtp) cc_final: 0.7649 (mmmt) REVERT: B 249 ASN cc_start: 0.7682 (t0) cc_final: 0.6922 (t0) REVERT: B 318 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8759 (pm20) outliers start: 8 outliers final: 6 residues processed: 77 average time/residue: 0.2051 time to fit residues: 20.7324 Evaluate side-chains 72 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 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 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 70 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 50 optimal weight: 0.0770 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3647 r_free = 0.3647 target = 0.076188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.054994 restraints weight = 23319.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.056762 restraints weight = 14083.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.057913 restraints weight = 10340.533| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5955 Z= 0.160 Angle : 0.609 9.712 8119 Z= 0.291 Chirality : 0.038 0.168 915 Planarity : 0.004 0.039 1049 Dihedral : 3.784 19.032 798 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.15 % Allowed : 15.49 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.32), residues: 729 helix: 1.16 (0.29), residues: 360 sheet: -0.34 (0.61), residues: 66 loop : -1.09 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 289 HIS 0.007 0.001 HIS B 88 PHE 0.009 0.001 PHE B 350 TYR 0.014 0.002 TYR B 108 ARG 0.007 0.000 ARG B 90 *********************** 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 78 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 94 GLU cc_start: 0.7986 (pt0) cc_final: 0.7453 (pt0) REVERT: B 172 LYS cc_start: 0.8074 (mmtp) cc_final: 0.7601 (mmmt) REVERT: B 249 ASN cc_start: 0.7710 (t0) cc_final: 0.6969 (t0) REVERT: B 318 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8737 (pm20) outliers start: 7 outliers final: 5 residues processed: 76 average time/residue: 0.1989 time to fit residues: 19.6997 Evaluate side-chains 73 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 54 optimal weight: 0.0010 chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3606 r_free = 0.3606 target = 0.074733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.053073 restraints weight = 23599.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.054816 restraints weight = 14167.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.055996 restraints weight = 10377.271| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5955 Z= 0.173 Angle : 0.618 10.892 8119 Z= 0.293 Chirality : 0.038 0.156 915 Planarity : 0.004 0.031 1049 Dihedral : 3.740 19.159 798 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.48 % Allowed : 16.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.32), residues: 729 helix: 1.19 (0.29), residues: 361 sheet: -0.12 (0.63), residues: 66 loop : -1.05 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 289 HIS 0.002 0.001 HIS A 55 PHE 0.016 0.001 PHE B 224 TYR 0.012 0.001 TYR B 108 ARG 0.003 0.000 ARG A 90 *********************** 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 81 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 57 GLU cc_start: 0.9050 (pt0) cc_final: 0.8636 (tp30) REVERT: A 315 MET cc_start: 0.7568 (mmt) cc_final: 0.7087 (mmm) REVERT: B 172 LYS cc_start: 0.8317 (mmtp) cc_final: 0.7777 (mmmt) REVERT: B 249 ASN cc_start: 0.7562 (t0) cc_final: 0.6716 (t0) REVERT: B 318 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8791 (pm20) outliers start: 9 outliers final: 5 residues processed: 80 average time/residue: 0.1898 time to fit residues: 20.2483 Evaluate side-chains 72 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 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 18 optimal weight: 0.6980 chunk 56 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3602 r_free = 0.3602 target = 0.074620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.052968 restraints weight = 23813.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.054713 restraints weight = 14249.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.055913 restraints weight = 10411.926| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5955 Z= 0.172 Angle : 0.636 10.026 8119 Z= 0.302 Chirality : 0.039 0.163 915 Planarity : 0.004 0.031 1049 Dihedral : 3.702 18.347 798 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.32 % Allowed : 17.96 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.32), residues: 729 helix: 1.28 (0.29), residues: 361 sheet: -0.11 (0.62), residues: 66 loop : -1.05 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 289 HIS 0.003 0.001 HIS A 55 PHE 0.018 0.001 PHE B 224 TYR 0.012 0.002 TYR B 108 ARG 0.004 0.000 ARG A 90 *********************** 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 80 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 315 MET cc_start: 0.7541 (mmt) cc_final: 0.7093 (mmm) REVERT: B 172 LYS cc_start: 0.8240 (mmtp) cc_final: 0.7699 (mmmt) REVERT: B 249 ASN cc_start: 0.7577 (t0) cc_final: 0.6788 (t0) REVERT: B 318 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8726 (pm20) outliers start: 8 outliers final: 7 residues processed: 77 average time/residue: 0.1871 time to fit residues: 19.0042 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 : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN 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 318 GLU 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 17 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.073967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.052385 restraints weight = 23712.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.054117 restraints weight = 14263.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.055306 restraints weight = 10439.819| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5955 Z= 0.191 Angle : 0.648 10.787 8119 Z= 0.307 Chirality : 0.039 0.183 915 Planarity : 0.004 0.031 1049 Dihedral : 3.718 18.759 798 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.48 % Allowed : 17.79 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.32), residues: 729 helix: 1.39 (0.29), residues: 355 sheet: -0.12 (0.62), residues: 66 loop : -1.00 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 289 HIS 0.002 0.001 HIS A 123 PHE 0.017 0.001 PHE B 224 TYR 0.011 0.001 TYR B 108 ARG 0.004 0.000 ARG A 90 *********************** 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 78 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.7669 (mmt) cc_final: 0.7217 (mmm) REVERT: B 172 LYS cc_start: 0.8294 (mmtp) cc_final: 0.7741 (mmmt) REVERT: B 249 ASN cc_start: 0.7502 (t0) cc_final: 0.6704 (t0) REVERT: B 318 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8701 (pm20) outliers start: 9 outliers final: 7 residues processed: 74 average time/residue: 0.1915 time to fit residues: 18.5841 Evaluate side-chains 75 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 61 SER Chi-restraints excluded: chain B residue 67 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 43 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.0170 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.073748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.052193 restraints weight = 23875.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.053930 restraints weight = 14304.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.055110 restraints weight = 10436.970| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4991 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= 0.194 Angle : 0.664 10.810 8119 Z= 0.312 Chirality : 0.039 0.214 915 Planarity : 0.004 0.031 1049 Dihedral : 3.741 19.893 798 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.48 % Allowed : 17.79 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.32), residues: 729 helix: 1.32 (0.29), residues: 360 sheet: -0.12 (0.61), residues: 66 loop : -1.01 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 289 HIS 0.003 0.001 HIS A 55 PHE 0.018 0.001 PHE B 224 TYR 0.011 0.001 TYR B 108 ARG 0.003 0.000 ARG A 90 *********************** 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 80 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: B 85 MET cc_start: 0.8117 (ppp) cc_final: 0.7833 (ppp) REVERT: B 172 LYS cc_start: 0.8312 (mmtp) cc_final: 0.7751 (mmmt) REVERT: B 249 ASN cc_start: 0.7547 (t0) cc_final: 0.6787 (t0) REVERT: B 318 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8668 (pm20) outliers start: 9 outliers final: 7 residues processed: 76 average time/residue: 0.2031 time to fit residues: 20.1027 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 : 0.649 ------------------------------------------------------------------------------- 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 61 SER Chi-restraints excluded: chain B residue 67 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 41 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.073813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.052369 restraints weight = 24137.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.054112 restraints weight = 14311.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.055297 restraints weight = 10408.725| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5955 Z= 0.186 Angle : 0.689 10.760 8119 Z= 0.322 Chirality : 0.040 0.220 915 Planarity : 0.004 0.030 1049 Dihedral : 3.735 18.640 798 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.32 % Allowed : 18.78 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.32), residues: 729 helix: 1.35 (0.29), residues: 360 sheet: -0.16 (0.61), residues: 66 loop : -1.02 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 289 HIS 0.008 0.001 HIS A 210 PHE 0.018 0.002 PHE B 224 TYR 0.012 0.002 TYR B 108 ARG 0.003 0.000 ARG A 90 ********************** 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 76 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8525 (tptp) cc_final: 0.8289 (tptp) REVERT: A 53 LEU cc_start: 0.9703 (mt) cc_final: 0.9376 (pp) REVERT: B 172 LYS cc_start: 0.8305 (mmtp) cc_final: 0.7741 (mmmt) REVERT: B 249 ASN cc_start: 0.7490 (t0) cc_final: 0.6710 (t0) outliers start: 8 outliers final: 7 residues processed: 73 average time/residue: 0.2014 time to fit residues: 19.1013 Evaluate side-chains 74 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 61 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 271 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 41 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 0.0470 chunk 4 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 0.0050 chunk 2 optimal weight: 0.0970 chunk 37 optimal weight: 2.9990 overall best weight: 0.7892 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.073647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.052266 restraints weight = 24010.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.053989 restraints weight = 14307.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.055163 restraints weight = 10428.115| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5274 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= 0.189 Angle : 0.693 12.433 8119 Z= 0.323 Chirality : 0.040 0.224 915 Planarity : 0.004 0.031 1049 Dihedral : 3.742 21.268 798 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.32 % Allowed : 19.11 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.33), residues: 729 helix: 1.34 (0.29), residues: 360 sheet: -0.11 (0.62), residues: 66 loop : -1.01 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 289 HIS 0.009 0.001 HIS A 210 PHE 0.018 0.001 PHE B 224 TYR 0.012 0.002 TYR B 108 ARG 0.003 0.000 ARG A 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2509.16 seconds wall clock time: 46 minutes 4.10 seconds (2764.10 seconds total)