Starting phenix.real_space_refine on Sun Jul 27 14:38:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eay_27990/07_2025/8eay_27990.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eay_27990/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8eay_27990/07_2025/8eay_27990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eay_27990/07_2025/8eay_27990.map" model { file = "/net/cci-nas-00/data/ceres_data/8eay_27990/07_2025/8eay_27990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eay_27990/07_2025/8eay_27990.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.101 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.91, per 1000 atoms: 0.52 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: 2.50 Conformation dependent library (CDL) restraints added in 624.1 milliseconds 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: 0.93 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: 3.35 Time building geometry restraints manager: 3.15 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: 1.320 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: 0.170 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.360 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.520 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (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 TRP 0.015 0.002 TRP A 309 HIS 0.001 0.000 HIS A 332 PHE 0.007 0.001 PHE A 334 TYR 0.017 0.002 TYR L 2 ARG 0.004 0.000 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.27536 ( 139) hydrogen bonds : angle 9.07110 ( 390) SS BOND : bond 0.03309 ( 9) SS BOND : angle 13.07970 ( 18) covalent geometry : bond 0.00797 ( 4841) covalent geometry : angle 1.13687 ( 6566) *********************** 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 : 0.797 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: 0.3440 time to fit residues: 34.2630 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 : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.0980 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4782 r_free = 0.4782 target = 0.229876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.191775 restraints weight = 15985.267| |-----------------------------------------------------------------------------| r_work (start): 0.4457 rms_B_bonded: 2.09 r_work: 0.4242 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4109 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4850 Z= 0.154 Angle : 0.656 10.162 6584 Z= 0.350 Chirality : 0.045 0.145 759 Planarity : 0.005 0.049 841 Dihedral : 5.089 24.455 676 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.52 % Favored : 89.32 % Rotamer: Outliers : 1.51 % Allowed : 6.81 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.34), residues: 618 helix: -0.12 (0.54), residues: 105 sheet: -0.80 (0.42), residues: 166 loop : -2.27 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP H 34 HIS 0.001 0.000 HIS A 368 PHE 0.011 0.001 PHE A 334 TYR 0.020 0.002 TYR H 50 ARG 0.004 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.05151 ( 139) hydrogen bonds : angle 6.38538 ( 390) SS BOND : bond 0.00611 ( 9) SS BOND : angle 1.88258 ( 18) covalent geometry : bond 0.00351 ( 4841) covalent geometry : angle 0.64973 ( 6566) *********************** 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: 8 poor density : 56 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 0.3804 time to fit residues: 31.0366 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 : 0.867 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4773 r_free = 0.4773 target = 0.228604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.191310 restraints weight = 16136.893| |-----------------------------------------------------------------------------| r_work (start): 0.4421 rms_B_bonded: 2.30 r_work: 0.4150 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4850 Z= 0.135 Angle : 0.606 9.657 6584 Z= 0.322 Chirality : 0.044 0.143 759 Planarity : 0.004 0.048 841 Dihedral : 4.916 21.420 676 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.71 % Favored : 90.13 % Rotamer: Outliers : 1.32 % Allowed : 10.21 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.34), residues: 618 helix: 0.23 (0.56), residues: 105 sheet: -1.10 (0.39), residues: 181 loop : -2.29 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 47 HIS 0.001 0.000 HIS A 368 PHE 0.007 0.001 PHE L 97 TYR 0.017 0.002 TYR H 33 ARG 0.003 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 139) hydrogen bonds : angle 5.86906 ( 390) SS BOND : bond 0.00337 ( 9) SS BOND : angle 1.42802 ( 18) covalent geometry : bond 0.00314 ( 4841) covalent geometry : angle 0.60266 ( 6566) *********************** 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 60 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 2 TYR cc_start: 0.7200 (t80) cc_final: 0.6173 (t80) outliers start: 7 outliers final: 6 residues processed: 58 average time/residue: 0.3692 time to fit residues: 27.9259 Evaluate side-chains 53 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 41 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4772 r_free = 0.4772 target = 0.229036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.190689 restraints weight = 16347.326| |-----------------------------------------------------------------------------| r_work (start): 0.4402 rms_B_bonded: 2.33 r_work: 0.4111 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4850 Z= 0.151 Angle : 0.600 9.574 6584 Z= 0.320 Chirality : 0.044 0.142 759 Planarity : 0.005 0.047 841 Dihedral : 5.042 23.454 676 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.68 % Favored : 89.16 % Rotamer: Outliers : 1.70 % Allowed : 13.04 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.34), residues: 618 helix: 0.31 (0.56), residues: 105 sheet: -1.16 (0.38), residues: 187 loop : -2.37 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 47 HIS 0.002 0.001 HIS A 368 PHE 0.007 0.001 PHE L 97 TYR 0.019 0.002 TYR H 33 ARG 0.004 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 139) hydrogen bonds : angle 5.72579 ( 390) SS BOND : bond 0.00354 ( 9) SS BOND : angle 1.33121 ( 18) covalent geometry : bond 0.00349 ( 4841) covalent geometry : angle 0.59645 ( 6566) *********************** 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 63 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6776 (mp) REVERT: L 2 TYR cc_start: 0.7097 (t80) cc_final: 0.6199 (t80) outliers start: 9 outliers final: 8 residues processed: 61 average time/residue: 0.4188 time to fit residues: 33.3787 Evaluate side-chains 59 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 3 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 10 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.0270 chunk 23 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- 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 = 0.4743 r_free = 0.4743 target = 0.226039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.176850 restraints weight = 16488.316| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 2.29 r_work: 0.4108 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3966 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4850 Z= 0.180 Angle : 0.637 9.460 6584 Z= 0.340 Chirality : 0.045 0.146 759 Planarity : 0.005 0.047 841 Dihedral : 5.200 22.220 676 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.65 % Favored : 88.19 % Rotamer: Outliers : 1.89 % Allowed : 15.50 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.33), residues: 618 helix: 0.33 (0.56), residues: 105 sheet: -1.25 (0.38), residues: 185 loop : -2.48 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 47 HIS 0.001 0.000 HIS A 332 PHE 0.009 0.001 PHE H 51 TYR 0.022 0.002 TYR H 33 ARG 0.004 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 139) hydrogen bonds : angle 5.72811 ( 390) SS BOND : bond 0.00342 ( 9) SS BOND : angle 1.26090 ( 18) covalent geometry : bond 0.00419 ( 4841) covalent geometry : angle 0.63413 ( 6566) *********************** 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 61 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 TYR cc_start: 0.6545 (m-80) cc_final: 0.5685 (m-80) outliers start: 10 outliers final: 7 residues processed: 59 average time/residue: 0.4083 time to fit residues: 31.7902 Evaluate side-chains 55 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 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 2 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 56 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 55 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4753 r_free = 0.4753 target = 0.226975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.188337 restraints weight = 16363.270| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 2.33 r_work: 0.4102 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3963 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4850 Z= 0.138 Angle : 0.585 9.046 6584 Z= 0.312 Chirality : 0.044 0.146 759 Planarity : 0.005 0.043 841 Dihedral : 5.075 23.369 676 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.00 % Favored : 88.83 % Rotamer: Outliers : 1.70 % Allowed : 16.26 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.33), residues: 618 helix: 0.40 (0.56), residues: 105 sheet: -1.23 (0.38), residues: 180 loop : -2.48 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.001 0.000 HIS A 368 PHE 0.007 0.001 PHE L 97 TYR 0.016 0.002 TYR H 33 ARG 0.002 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 139) hydrogen bonds : angle 5.59261 ( 390) SS BOND : bond 0.00274 ( 9) SS BOND : angle 1.13629 ( 18) covalent geometry : bond 0.00320 ( 4841) covalent geometry : angle 0.58279 ( 6566) *********************** 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 62 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 GLN cc_start: 0.6922 (mm-40) cc_final: 0.6568 (tm-30) REVERT: L 2 TYR cc_start: 0.7508 (t80) cc_final: 0.6315 (t80) outliers start: 9 outliers final: 8 residues processed: 59 average time/residue: 0.3955 time to fit residues: 30.4120 Evaluate side-chains 58 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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 349 GLU Chi-restraints excluded: chain A residue 388 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 15 optimal weight: 0.0870 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.4762 r_free = 0.4762 target = 0.227960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.190358 restraints weight = 16424.843| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 2.39 r_work: 0.4110 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2838 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= 0.121 Angle : 0.573 8.456 6584 Z= 0.304 Chirality : 0.044 0.145 759 Planarity : 0.004 0.043 841 Dihedral : 4.954 22.260 676 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.68 % Favored : 89.16 % Rotamer: Outliers : 1.89 % Allowed : 16.45 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.33), residues: 618 helix: 0.43 (0.56), residues: 105 sheet: -1.22 (0.38), residues: 180 loop : -2.42 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS A 332 PHE 0.007 0.001 PHE L 97 TYR 0.019 0.002 TYR A 359 ARG 0.001 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 139) hydrogen bonds : angle 5.46105 ( 390) SS BOND : bond 0.00285 ( 9) SS BOND : angle 1.05800 ( 18) covalent geometry : bond 0.00280 ( 4841) covalent geometry : angle 0.57086 ( 6566) *********************** 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 60 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 THR cc_start: 0.6516 (OUTLIER) cc_final: 0.6149 (m) REVERT: A 310 TYR cc_start: 0.6348 (m-80) cc_final: 0.5764 (m-80) REVERT: H 1 GLN cc_start: 0.6754 (mm-40) cc_final: 0.6532 (tm-30) REVERT: L 2 TYR cc_start: 0.7246 (t80) cc_final: 0.6670 (t80) outliers start: 10 outliers final: 8 residues processed: 57 average time/residue: 0.3639 time to fit residues: 26.8040 Evaluate side-chains 58 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 349 GLU Chi-restraints excluded: chain A residue 388 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 0.4980 chunk 7 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 0.0010 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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 = 0.4776 r_free = 0.4776 target = 0.229531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.187709 restraints weight = 16463.443| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 2.46 r_work: 0.4151 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.4014 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4850 Z= 0.107 Angle : 0.553 7.797 6584 Z= 0.293 Chirality : 0.043 0.144 759 Planarity : 0.004 0.044 841 Dihedral : 4.758 21.972 676 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.71 % Favored : 90.13 % Rotamer: Outliers : 2.46 % Allowed : 16.07 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.33), residues: 618 helix: 0.45 (0.56), residues: 105 sheet: -1.28 (0.37), residues: 186 loop : -2.32 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS A 368 PHE 0.007 0.001 PHE L 97 TYR 0.014 0.001 TYR A 359 ARG 0.001 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.02881 ( 139) hydrogen bonds : angle 5.28244 ( 390) SS BOND : bond 0.00228 ( 9) SS BOND : angle 0.98861 ( 18) covalent geometry : bond 0.00248 ( 4841) covalent geometry : angle 0.55104 ( 6566) *********************** 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 65 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 THR cc_start: 0.6496 (OUTLIER) cc_final: 0.6146 (m) REVERT: A 142 LYS cc_start: 0.8393 (tmmt) cc_final: 0.8156 (pttp) REVERT: A 226 GLU cc_start: 0.6127 (mt-10) cc_final: 0.5808 (mp0) REVERT: A 349 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6881 (tt0) REVERT: H 1 GLN cc_start: 0.7059 (mm-40) cc_final: 0.6657 (tm-30) REVERT: L 2 TYR cc_start: 0.7306 (t80) cc_final: 0.6735 (t80) outliers start: 13 outliers final: 10 residues processed: 61 average time/residue: 0.3600 time to fit residues: 28.4717 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 : 0.724 ------------------------------------------------------------------------------- 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 349 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 73 MET 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 7 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 45 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 56 optimal weight: 0.0030 chunk 26 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 = 0.4754 r_free = 0.4754 target = 0.227511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.186018 restraints weight = 16434.567| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 2.73 r_work: 0.4132 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3990 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4850 Z= 0.114 Angle : 0.563 7.473 6584 Z= 0.298 Chirality : 0.044 0.143 759 Planarity : 0.004 0.045 841 Dihedral : 4.736 22.075 676 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.19 % Favored : 89.64 % Rotamer: Outliers : 2.46 % Allowed : 16.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.33), residues: 618 helix: 0.48 (0.56), residues: 105 sheet: -1.29 (0.37), residues: 185 loop : -2.30 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.000 0.000 HIS A 368 PHE 0.007 0.001 PHE L 97 TYR 0.013 0.001 TYR H 50 ARG 0.001 0.000 ARG H 94 Details of bonding type rmsd hydrogen bonds : bond 0.02913 ( 139) hydrogen bonds : angle 5.23249 ( 390) SS BOND : bond 0.00242 ( 9) SS BOND : angle 1.42904 ( 18) covalent geometry : bond 0.00265 ( 4841) covalent geometry : angle 0.55838 ( 6566) *********************** 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 61 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 THR cc_start: 0.6525 (OUTLIER) cc_final: 0.6176 (m) REVERT: A 142 LYS cc_start: 0.8363 (tmmt) cc_final: 0.8135 (pttp) REVERT: A 349 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6957 (tt0) REVERT: H 1 GLN cc_start: 0.7108 (mm-40) cc_final: 0.6681 (tm-30) REVERT: L 2 TYR cc_start: 0.7327 (t80) cc_final: 0.6731 (t80) outliers start: 13 outliers final: 10 residues processed: 57 average time/residue: 0.3751 time to fit residues: 27.7641 Evaluate side-chains 60 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 349 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 73 MET 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 7 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4759 r_free = 0.4759 target = 0.227947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.186261 restraints weight = 16524.287| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 2.67 r_work: 0.4131 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3994 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4850 Z= 0.112 Angle : 0.558 6.922 6584 Z= 0.296 Chirality : 0.043 0.143 759 Planarity : 0.004 0.045 841 Dihedral : 4.683 22.100 676 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.87 % Favored : 89.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.34), residues: 618 helix: 0.50 (0.56), residues: 105 sheet: -1.25 (0.37), residues: 185 loop : -2.27 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.000 0.000 HIS A 368 PHE 0.006 0.001 PHE L 97 TYR 0.013 0.001 TYR H 50 ARG 0.004 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.02908 ( 139) hydrogen bonds : angle 5.18134 ( 390) SS BOND : bond 0.00233 ( 9) SS BOND : angle 1.32192 ( 18) covalent geometry : bond 0.00260 ( 4841) covalent geometry : angle 0.55399 ( 6566) ********************** 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 : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 THR cc_start: 0.6511 (OUTLIER) cc_final: 0.6167 (m) REVERT: A 349 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6724 (tt0) REVERT: H 1 GLN cc_start: 0.7090 (mm-40) cc_final: 0.6680 (tm-30) REVERT: L 2 TYR cc_start: 0.7339 (t80) cc_final: 0.6723 (t80) outliers start: 12 outliers final: 9 residues processed: 61 average time/residue: 0.4149 time to fit residues: 33.8609 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 : 0.693 ------------------------------------------------------------------------------- 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 349 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 73 MET 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 11 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 7 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4747 r_free = 0.4747 target = 0.226684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.184567 restraints weight = 16480.013| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 2.22 r_work: 0.4133 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4002 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.3188 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= 0.129 Angle : 0.575 6.738 6584 Z= 0.305 Chirality : 0.044 0.145 759 Planarity : 0.004 0.046 841 Dihedral : 4.757 22.618 676 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.00 % Favored : 88.83 % Rotamer: Outliers : 2.27 % Allowed : 17.20 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.33), residues: 618 helix: 0.48 (0.56), residues: 105 sheet: -1.28 (0.37), residues: 185 loop : -2.28 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.000 0.000 HIS A 368 PHE 0.006 0.001 PHE L 97 TYR 0.015 0.002 TYR H 50 ARG 0.001 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.02973 ( 139) hydrogen bonds : angle 5.18662 ( 390) SS BOND : bond 0.00243 ( 9) SS BOND : angle 1.24207 ( 18) covalent geometry : bond 0.00302 ( 4841) covalent geometry : angle 0.57195 ( 6566) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6060.12 seconds wall clock time: 107 minutes 9.51 seconds (6429.51 seconds total)