Starting phenix.real_space_refine on Sat Aug 23 03:31:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eay_27990/08_2025/8eay_27990.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eay_27990/08_2025/8eay_27990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8eay_27990/08_2025/8eay_27990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eay_27990/08_2025/8eay_27990.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eay_27990/08_2025/8eay_27990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eay_27990/08_2025/8eay_27990.map" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 33 5.16 5 C 2979 2.51 5 N 814 2.21 5 O 935 1.98 5 H 4718 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9479 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 6062 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 1 Chain: "H" Number of atoms: 1859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1859 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "L" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1558 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Time building chain proxies: 1.42, per 1000 atoms: 0.15 Number of scatterers: 9479 At special positions: 0 Unit cell: (74.37, 85.47, 134.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 O 935 8.00 N 814 7.00 C 2979 6.00 H 4718 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 407 " distance=2.13 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 308.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1150 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 12 sheets defined 18.1% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 67 through 89 removed outlier: 3.590A pdb=" N ASP A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 130 removed outlier: 3.790A pdb=" N VAL A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 188 through 196 removed outlier: 4.338A pdb=" N SER A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 237 through 247 removed outlier: 3.865A pdb=" N ILE A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 346 through 351 removed outlier: 4.058A pdb=" N GLU A 349 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 351 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.774A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 24 removed outlier: 4.353A pdb=" N GLY A 34 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N CYS A 283 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TRP A 309 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 320 " --> pdb=" O TRP A 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 149 removed outlier: 3.523A pdb=" N ALA A 147 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 159 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU A 39 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE A 275 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TRP A 43 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU A 273 " --> pdb=" O TRP A 43 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR A 45 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 271 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL A 47 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR A 269 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR A 49 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL A 267 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N SER A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL A 262 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 268 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 149 removed outlier: 3.523A pdb=" N ALA A 147 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 159 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS A 332 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 327 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 374 removed outlier: 3.645A pdb=" N VAL A 382 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 408 " --> pdb=" O VAL A 382 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 399 through 402 removed outlier: 3.595A pdb=" N ILE A 400 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE A 392 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.747A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.589A pdb=" N ILE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 9 through 12 removed outlier: 7.166A pdb=" N VAL L 11 " --> pdb=" O THR L 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB2, first strand: chain 'L' and resid 35 through 37 removed outlier: 6.907A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE L 47 " --> pdb=" O TRP L 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 89 through 90 removed outlier: 3.892A pdb=" N VAL L 96 " --> pdb=" O ALA L 90 " (cutoff:3.500A) 150 hydrogen bonds defined for protein. 390 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: 1.38 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4715 1.04 - 1.24: 565 1.24 - 1.43: 1481 1.43 - 1.63: 2752 1.63 - 1.83: 46 Bond restraints: 9559 Sorted by residual: bond pdb=" C PRO H 100C" pdb=" O PRO H 100C" ideal model delta sigma weight residual 1.235 1.062 0.173 1.30e-02 5.92e+03 1.77e+02 bond pdb=" C SER A 27 " pdb=" N CYS A 28 " ideal model delta sigma weight residual 1.332 1.509 -0.177 1.40e-02 5.10e+03 1.59e+02 bond pdb=" C CYS A 28 " pdb=" N SER A 29 " ideal model delta sigma weight residual 1.331 1.468 -0.137 1.41e-02 5.03e+03 9.48e+01 bond pdb=" C GLY A 406 " pdb=" N CYS A 407 " ideal model delta sigma weight residual 1.331 1.449 -0.118 1.37e-02 5.33e+03 7.45e+01 bond pdb=" N PRO H 100C" pdb=" CA PRO H 100C" ideal model delta sigma weight residual 1.469 1.370 0.099 1.28e-02 6.10e+03 5.97e+01 ... (remaining 9554 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.63: 17236 8.63 - 17.25: 15 17.25 - 25.88: 1 25.88 - 34.51: 2 34.51 - 43.13: 1 Bond angle restraints: 17255 Sorted by residual: angle pdb=" C PRO H 9 " pdb=" CA PRO H 9 " pdb=" HA PRO H 9 " ideal model delta sigma weight residual 109.00 65.87 43.13 3.00e+00 1.11e-01 2.07e+02 angle pdb=" N PRO H 9 " pdb=" CA PRO H 9 " pdb=" C PRO H 9 " ideal model delta sigma weight residual 112.47 139.07 -26.60 2.06e+00 2.36e-01 1.67e+02 angle pdb=" C MET L 46 " pdb=" N ILE L 47 " pdb=" CA ILE L 47 " ideal model delta sigma weight residual 123.16 136.84 -13.68 1.06e+00 8.90e-01 1.66e+02 angle pdb=" CA SER H 100 " pdb=" C SER H 100 " pdb=" N GLY H 100A" ideal model delta sigma weight residual 115.51 127.24 -11.73 1.08e+00 8.57e-01 1.18e+02 angle pdb=" N GLY H 10 " pdb=" CA GLY H 10 " pdb=" HA2 GLY H 10 " ideal model delta sigma weight residual 110.00 78.56 31.44 3.00e+00 1.11e-01 1.10e+02 ... (remaining 17250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4075 17.88 - 35.77: 299 35.77 - 53.65: 116 53.65 - 71.54: 34 71.54 - 89.42: 11 Dihedral angle restraints: 4535 sinusoidal: 2498 harmonic: 2037 Sorted by residual: dihedral pdb=" N PRO H 9 " pdb=" C PRO H 9 " pdb=" CA PRO H 9 " pdb=" CB PRO H 9 " ideal model delta harmonic sigma weight residual 115.10 157.65 -42.55 0 2.50e+00 1.60e-01 2.90e+02 dihedral pdb=" C PRO H 9 " pdb=" N PRO H 9 " pdb=" CA PRO H 9 " pdb=" CB PRO H 9 " ideal model delta harmonic sigma weight residual -120.70 -159.13 38.43 0 2.50e+00 1.60e-01 2.36e+02 dihedral pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " pdb=" SG CYS A 339 " pdb=" CB CYS A 339 " ideal model delta sinusoidal sigma weight residual 93.00 11.25 81.75 1 1.00e+01 1.00e-02 8.22e+01 ... (remaining 4532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.388: 758 0.388 - 0.777: 0 0.777 - 1.165: 0 1.165 - 1.553: 0 1.553 - 1.942: 1 Chirality restraints: 759 Sorted by residual: chirality pdb=" CA PRO H 9 " pdb=" N PRO H 9 " pdb=" C PRO H 9 " pdb=" CB PRO H 9 " both_signs ideal model delta sigma weight residual False 2.72 0.78 1.94 2.00e-01 2.50e+01 9.43e+01 chirality pdb=" CA MET H 100B" pdb=" N MET H 100B" pdb=" C MET H 100B" pdb=" CB MET H 100B" both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA GLN L 50 " pdb=" N GLN L 50 " pdb=" C GLN L 50 " pdb=" CB GLN L 50 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 756 not shown) Planarity restraints: 1439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN L 38 " -0.008 2.00e-02 2.50e+03 4.30e-01 2.77e+03 pdb=" CD GLN L 38 " -0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN L 38 " 0.008 2.00e-02 2.50e+03 pdb=" NE2 GLN L 38 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN L 38 " -0.744 2.00e-02 2.50e+03 pdb="HE22 GLN L 38 " 0.745 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 382 " 0.032 2.00e-02 2.50e+03 5.87e-02 3.44e+01 pdb=" N ALA A 383 " -0.101 2.00e-02 2.50e+03 pdb=" CA ALA A 383 " 0.026 2.00e-02 2.50e+03 pdb=" H ALA A 383 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 45 " -0.028 2.00e-02 2.50e+03 5.31e-02 2.82e+01 pdb=" C VAL L 45 " 0.092 2.00e-02 2.50e+03 pdb=" O VAL L 45 " -0.033 2.00e-02 2.50e+03 pdb=" N MET L 46 " -0.031 2.00e-02 2.50e+03 ... (remaining 1436 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 219 2.06 - 2.69: 14539 2.69 - 3.33: 25347 3.33 - 3.96: 33012 3.96 - 4.60: 50197 Nonbonded interactions: 123314 Sorted by model distance: nonbonded pdb=" HH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 1.420 2.450 nonbonded pdb=" HB3 CYS A 113 " pdb=" HB2 CYS A 339 " model vdw 1.454 2.440 nonbonded pdb=" O TYR A 263 " pdb=" HG SER A 266 " model vdw 1.522 2.450 nonbonded pdb="HE22 GLN A 88 " pdb=" O ALA A 211 " model vdw 1.551 2.450 nonbonded pdb=" OE1 GLN L 37 " pdb=" HZ2 LYS L 39 " model vdw 1.560 2.450 ... (remaining 123309 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.060 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.820 Find NCS groups from input model: 0.020 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 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 : 0.008 0.177 4850 Z= 0.525 Angle : 1.325 52.897 6584 Z= 0.765 Chirality : 0.089 1.942 759 Planarity : 0.008 0.111 841 Dihedral : 14.180 76.735 1766 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.55 % Favored : 90.13 % Rotamer: Outliers : 0.76 % Allowed : 2.08 % Favored : 97.16 % Cbeta Deviations : 0.70 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.34), residues: 618 helix: -1.12 (0.52), residues: 101 sheet: -0.77 (0.42), residues: 172 loop : -2.15 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 367 TYR 0.017 0.002 TYR L 2 PHE 0.007 0.001 PHE A 334 TRP 0.015 0.002 TRP A 309 HIS 0.001 0.000 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00797 ( 4841) covalent geometry : angle 1.13687 ( 6566) SS BOND : bond 0.03309 ( 9) SS BOND : angle 13.07970 ( 18) hydrogen bonds : bond 0.27536 ( 139) hydrogen bonds : angle 9.07110 ( 390) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 77 average time/residue: 0.1093 time to fit residues: 10.8957 Evaluate side-chains 50 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.227933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.189507 restraints weight = 16120.808| |-----------------------------------------------------------------------------| r_work (start): 0.4456 rms_B_bonded: 2.12 r_work: 0.4234 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4102 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4850 Z= 0.151 Angle : 0.651 9.989 6584 Z= 0.348 Chirality : 0.045 0.148 759 Planarity : 0.005 0.049 841 Dihedral : 5.094 24.612 676 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.19 % Favored : 89.64 % Rotamer: Outliers : 1.32 % Allowed : 6.81 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.34), residues: 618 helix: -0.11 (0.55), residues: 105 sheet: -0.79 (0.42), residues: 166 loop : -2.27 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 304 TYR 0.019 0.002 TYR H 50 PHE 0.012 0.001 PHE A 334 TRP 0.006 0.002 TRP H 34 HIS 0.001 0.000 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 4841) covalent geometry : angle 0.64610 ( 6566) SS BOND : bond 0.00496 ( 9) SS BOND : angle 1.70961 ( 18) hydrogen bonds : bond 0.05023 ( 139) hydrogen bonds : angle 6.39502 ( 390) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 0.1165 time to fit residues: 9.3355 Evaluate side-chains 56 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 1 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4792 r_free = 0.4792 target = 0.231485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.192600 restraints weight = 16366.395| |-----------------------------------------------------------------------------| r_work (start): 0.4416 rms_B_bonded: 2.47 r_work: 0.4149 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4850 Z= 0.134 Angle : 0.603 9.769 6584 Z= 0.321 Chirality : 0.044 0.145 759 Planarity : 0.005 0.048 841 Dihedral : 4.929 21.414 676 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.87 % Favored : 89.97 % Rotamer: Outliers : 1.32 % Allowed : 10.40 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.34), residues: 618 helix: 0.20 (0.56), residues: 105 sheet: -1.06 (0.40), residues: 181 loop : -2.32 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 304 TYR 0.017 0.002 TYR H 33 PHE 0.007 0.001 PHE H 78 TRP 0.006 0.001 TRP H 47 HIS 0.001 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 4841) covalent geometry : angle 0.59946 ( 6566) SS BOND : bond 0.00340 ( 9) SS BOND : angle 1.37779 ( 18) hydrogen bonds : bond 0.03951 ( 139) hydrogen bonds : angle 5.86976 ( 390) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 2 TYR cc_start: 0.7226 (t80) cc_final: 0.6183 (t80) outliers start: 7 outliers final: 6 residues processed: 59 average time/residue: 0.1320 time to fit residues: 9.9364 Evaluate side-chains 55 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 1 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 39 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.4731 r_free = 0.4731 target = 0.224367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.182700 restraints weight = 16611.430| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 2.28 r_work: 0.4058 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 4850 Z= 0.214 Angle : 0.668 10.237 6584 Z= 0.358 Chirality : 0.046 0.144 759 Planarity : 0.005 0.047 841 Dihedral : 5.415 24.531 676 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.43 % Favored : 86.41 % Rotamer: Outliers : 1.51 % Allowed : 14.56 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (0.33), residues: 618 helix: 0.23 (0.55), residues: 105 sheet: -1.18 (0.39), residues: 180 loop : -2.52 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 304 TYR 0.025 0.002 TYR H 50 PHE 0.010 0.002 PHE H 51 TRP 0.008 0.002 TRP H 103 HIS 0.002 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 4841) covalent geometry : angle 0.66466 ( 6566) SS BOND : bond 0.00419 ( 9) SS BOND : angle 1.47686 ( 18) hydrogen bonds : bond 0.04146 ( 139) hydrogen bonds : angle 5.96301 ( 390) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 GLN cc_start: 0.6894 (mm110) cc_final: 0.6694 (tm-30) outliers start: 8 outliers final: 8 residues processed: 60 average time/residue: 0.1201 time to fit residues: 9.2445 Evaluate side-chains 59 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain L residue 1 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 56 optimal weight: 0.1980 chunk 38 optimal weight: 0.0040 chunk 49 optimal weight: 0.0980 chunk 31 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.3392 ------------------------------------------------------------------------------- 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 = 0.4793 r_free = 0.4793 target = 0.231270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.190005 restraints weight = 16324.856| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 2.82 r_work: 0.4164 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.4025 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4850 Z= 0.103 Angle : 0.558 9.071 6584 Z= 0.298 Chirality : 0.043 0.146 759 Planarity : 0.004 0.044 841 Dihedral : 4.931 21.048 676 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.90 % Favored : 90.94 % Rotamer: Outliers : 1.70 % Allowed : 15.31 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.34), residues: 618 helix: 0.40 (0.56), residues: 105 sheet: -1.16 (0.39), residues: 183 loop : -2.39 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 94 TYR 0.013 0.001 TYR H 91 PHE 0.006 0.001 PHE L 97 TRP 0.008 0.001 TRP H 47 HIS 0.001 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 4841) covalent geometry : angle 0.55583 ( 6566) SS BOND : bond 0.00237 ( 9) SS BOND : angle 1.04892 ( 18) hydrogen bonds : bond 0.03200 ( 139) hydrogen bonds : angle 5.58685 ( 390) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6675 (mp) REVERT: A 310 TYR cc_start: 0.6481 (m-80) cc_final: 0.5783 (m-80) REVERT: H 1 GLN cc_start: 0.7092 (mm110) cc_final: 0.6729 (tm-30) REVERT: L 2 TYR cc_start: 0.7282 (t80) cc_final: 0.6175 (t80) outliers start: 9 outliers final: 8 residues processed: 59 average time/residue: 0.1229 time to fit residues: 9.4938 Evaluate side-chains 61 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain L residue 1 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4758 r_free = 0.4758 target = 0.227555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.191332 restraints weight = 16473.327| |-----------------------------------------------------------------------------| r_work (start): 0.4406 rms_B_bonded: 2.30 r_work: 0.4101 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3971 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4850 Z= 0.142 Angle : 0.583 9.098 6584 Z= 0.311 Chirality : 0.044 0.142 759 Planarity : 0.004 0.045 841 Dihedral : 4.968 23.119 676 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.68 % Favored : 89.16 % Rotamer: Outliers : 2.27 % Allowed : 14.93 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.34), residues: 618 helix: 0.44 (0.56), residues: 105 sheet: -1.10 (0.39), residues: 180 loop : -2.45 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 304 TYR 0.017 0.002 TYR H 33 PHE 0.007 0.001 PHE L 97 TRP 0.008 0.002 TRP H 47 HIS 0.001 0.000 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4841) covalent geometry : angle 0.58046 ( 6566) SS BOND : bond 0.00288 ( 9) SS BOND : angle 1.10827 ( 18) hydrogen bonds : bond 0.03318 ( 139) hydrogen bonds : angle 5.56306 ( 390) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.8455 (tmmt) cc_final: 0.8252 (pttp) REVERT: H 1 GLN cc_start: 0.7118 (mm110) cc_final: 0.6722 (tm-30) REVERT: L 2 TYR cc_start: 0.7514 (t80) cc_final: 0.6319 (t80) outliers start: 12 outliers final: 8 residues processed: 60 average time/residue: 0.1301 time to fit residues: 9.9698 Evaluate side-chains 59 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain L residue 1 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.225279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.175715 restraints weight = 16492.868| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 2.34 r_work: 0.4117 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3970 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4850 Z= 0.150 Angle : 0.592 9.004 6584 Z= 0.316 Chirality : 0.044 0.145 759 Planarity : 0.005 0.044 841 Dihedral : 5.005 22.906 676 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.52 % Favored : 89.32 % Rotamer: Outliers : 2.84 % Allowed : 15.31 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.29 (0.33), residues: 618 helix: 0.43 (0.56), residues: 105 sheet: -1.14 (0.38), residues: 180 loop : -2.46 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.018 0.002 TYR H 33 PHE 0.006 0.001 PHE L 97 TRP 0.007 0.002 TRP H 47 HIS 0.000 0.000 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 4841) covalent geometry : angle 0.58992 ( 6566) SS BOND : bond 0.00275 ( 9) SS BOND : angle 1.08049 ( 18) hydrogen bonds : bond 0.03305 ( 139) hydrogen bonds : angle 5.53378 ( 390) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 THR cc_start: 0.6499 (OUTLIER) cc_final: 0.6126 (m) REVERT: H 1 GLN cc_start: 0.7148 (mm110) cc_final: 0.6730 (tm-30) REVERT: L 2 TYR cc_start: 0.7415 (t80) cc_final: 0.6788 (t80) outliers start: 15 outliers final: 11 residues processed: 62 average time/residue: 0.1182 time to fit residues: 9.7435 Evaluate side-chains 63 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain L residue 1 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 35 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.225965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.188058 restraints weight = 16433.584| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 2.41 r_work: 0.4089 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4850 Z= 0.147 Angle : 0.592 8.448 6584 Z= 0.315 Chirality : 0.044 0.147 759 Planarity : 0.005 0.044 841 Dihedral : 5.054 27.640 676 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.49 % Favored : 88.35 % Rotamer: Outliers : 2.46 % Allowed : 16.45 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.30 (0.33), residues: 618 helix: 0.40 (0.56), residues: 105 sheet: -1.16 (0.38), residues: 180 loop : -2.46 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.020 0.002 TYR A 359 PHE 0.007 0.001 PHE L 97 TRP 0.008 0.002 TRP H 47 HIS 0.001 0.000 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 4841) covalent geometry : angle 0.58962 ( 6566) SS BOND : bond 0.00375 ( 9) SS BOND : angle 1.08534 ( 18) hydrogen bonds : bond 0.03224 ( 139) hydrogen bonds : angle 5.48415 ( 390) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 THR cc_start: 0.6507 (OUTLIER) cc_final: 0.6143 (m) REVERT: H 1 GLN cc_start: 0.6955 (mm110) cc_final: 0.6671 (tm-30) REVERT: L 2 TYR cc_start: 0.7223 (t80) cc_final: 0.7022 (t80) outliers start: 13 outliers final: 11 residues processed: 61 average time/residue: 0.1221 time to fit residues: 9.7041 Evaluate side-chains 64 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain L residue 1 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 15 optimal weight: 0.0270 chunk 28 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.226539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.185232 restraints weight = 16492.744| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 2.19 r_work: 0.4116 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3971 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4850 Z= 0.120 Angle : 0.566 8.148 6584 Z= 0.301 Chirality : 0.044 0.145 759 Planarity : 0.004 0.044 841 Dihedral : 4.941 26.175 676 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.22 % Favored : 90.61 % Rotamer: Outliers : 2.27 % Allowed : 17.01 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.33), residues: 618 helix: 0.43 (0.56), residues: 105 sheet: -1.17 (0.38), residues: 180 loop : -2.40 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 205 TYR 0.015 0.002 TYR A 359 PHE 0.007 0.001 PHE L 97 TRP 0.008 0.001 TRP H 47 HIS 0.000 0.000 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 4841) covalent geometry : angle 0.56438 ( 6566) SS BOND : bond 0.00263 ( 9) SS BOND : angle 1.00781 ( 18) hydrogen bonds : bond 0.03013 ( 139) hydrogen bonds : angle 5.36061 ( 390) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 THR cc_start: 0.6556 (OUTLIER) cc_final: 0.6203 (m) REVERT: A 142 LYS cc_start: 0.8408 (tmmt) cc_final: 0.8161 (pttp) REVERT: H 1 GLN cc_start: 0.7199 (mm110) cc_final: 0.6754 (tm-30) outliers start: 12 outliers final: 10 residues processed: 58 average time/residue: 0.1260 time to fit residues: 9.4484 Evaluate side-chains 60 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain L residue 1 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.224746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.183078 restraints weight = 16350.416| |-----------------------------------------------------------------------------| r_work (start): 0.4328 rms_B_bonded: 2.39 r_work: 0.4098 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3955 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4850 Z= 0.146 Angle : 0.591 7.920 6584 Z= 0.315 Chirality : 0.044 0.145 759 Planarity : 0.005 0.046 841 Dihedral : 4.994 26.437 676 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.97 % Favored : 87.86 % Rotamer: Outliers : 2.27 % Allowed : 16.64 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.29 (0.33), residues: 618 helix: 0.41 (0.56), residues: 105 sheet: -1.21 (0.38), residues: 180 loop : -2.43 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 252 TYR 0.017 0.002 TYR H 50 PHE 0.007 0.001 PHE L 97 TRP 0.008 0.001 TRP H 47 HIS 0.000 0.000 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 4841) covalent geometry : angle 0.58929 ( 6566) SS BOND : bond 0.00295 ( 9) SS BOND : angle 1.02935 ( 18) hydrogen bonds : bond 0.03188 ( 139) hydrogen bonds : angle 5.38965 ( 390) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 THR cc_start: 0.6561 (OUTLIER) cc_final: 0.6197 (m) REVERT: A 142 LYS cc_start: 0.8394 (tmmt) cc_final: 0.8129 (pttp) REVERT: H 1 GLN cc_start: 0.7118 (mm110) cc_final: 0.6717 (tm-30) outliers start: 12 outliers final: 11 residues processed: 60 average time/residue: 0.1157 time to fit residues: 9.0134 Evaluate side-chains 61 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain L residue 1 SER Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 2 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4730 r_free = 0.4730 target = 0.224637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.183045 restraints weight = 16417.899| |-----------------------------------------------------------------------------| r_work (start): 0.4328 rms_B_bonded: 2.39 r_work: 0.4098 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3956 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.171 4850 Z= 0.244 Angle : 1.128 59.178 6584 Z= 0.687 Chirality : 0.044 0.152 759 Planarity : 0.004 0.046 841 Dihedral : 5.000 26.436 676 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.81 % Favored : 88.03 % Rotamer: Outliers : 2.08 % Allowed : 17.01 % Favored : 80.91 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.30 (0.33), residues: 618 helix: 0.42 (0.56), residues: 105 sheet: -1.21 (0.38), residues: 180 loop : -2.43 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 252 TYR 0.017 0.002 TYR H 50 PHE 0.007 0.001 PHE L 97 TRP 0.008 0.001 TRP H 47 HIS 0.001 0.000 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 4841) covalent geometry : angle 1.12813 ( 6566) SS BOND : bond 0.00261 ( 9) SS BOND : angle 1.02027 ( 18) hydrogen bonds : bond 0.03161 ( 139) hydrogen bonds : angle 5.38870 ( 390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2183.07 seconds wall clock time: 37 minutes 33.11 seconds (2253.11 seconds total)