Starting phenix.real_space_refine on Fri Aug 22 19:30:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fex_29033/08_2025/8fex_29033_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fex_29033/08_2025/8fex_29033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fex_29033/08_2025/8fex_29033_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fex_29033/08_2025/8fex_29033_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fex_29033/08_2025/8fex_29033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fex_29033/08_2025/8fex_29033.map" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 4730 2.51 5 N 1208 2.21 5 O 1342 1.98 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: 7302 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3604 Classifications: {'peptide': 433} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 420} Chain: "B" Number of atoms: 3698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3698 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 434} Chain breaks: 1 Time building chain proxies: 2.43, per 1000 atoms: 0.33 Number of scatterers: 7302 At special positions: 0 Unit cell: (75.3927, 84.4826, 129.932, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 1342 8.00 N 1208 7.00 C 4730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 471.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 8 sheets defined 38.7% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.960A pdb=" N ASN A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.540A pdb=" N ASN A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 146 through 159 removed outlier: 4.381A pdb=" N SER A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 257 through 280 removed outlier: 3.749A pdb=" N LYS A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 308 removed outlier: 3.565A pdb=" N ASP A 303 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 304 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N PHE A 305 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLU A 306 " --> pdb=" O ASP A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 368 removed outlier: 3.628A pdb=" N ASN A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 385 Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.738A pdb=" N ALA A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 46 through 62 Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 97 through 106 Processing helix chain 'B' and resid 109 through 132 removed outlier: 3.736A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 248 through 264 removed outlier: 3.546A pdb=" N ALA B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 351 Processing helix chain 'B' and resid 366 through 374 removed outlier: 3.601A pdb=" N TRP B 370 " --> pdb=" O ASN B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 477 through 482 removed outlier: 4.195A pdb=" N PHE B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 493 Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 removed outlier: 3.691A pdb=" N TRP A 33 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS A 4 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU A 61 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL A 63 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER A 8 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N ILE A 95 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE A 60 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU A 97 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 62 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 180 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 170 through 180 current: chain 'A' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 291 through 294 current: chain 'A' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 334 through 337 current: chain 'A' and resid 400 through 411 removed outlier: 9.761A pdb=" N LYS B 2 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LYS A 409 " --> pdb=" O LYS B 2 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 214 through 216 Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 6 removed outlier: 6.467A pdb=" N SER B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ILE B 443 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N SER B 389 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ILE B 445 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR B 387 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL B 357 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL B 386 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE B 359 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ILE B 388 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA B 361 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU B 281 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 501 " --> pdb=" O VAL B 312 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 18 through 20 Processing sheet with id=AA6, first strand: chain 'B' and resid 94 through 95 removed outlier: 5.999A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N PHE B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL B 141 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 285 through 287 Processing sheet with id=AA8, first strand: chain 'B' and resid 425 through 426 removed outlier: 3.795A pdb=" N THR B 431 " --> pdb=" O VAL B 426 " (cutoff:3.500A) 255 hydrogen bonds defined for protein. 702 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: 1.24 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2293 1.34 - 1.46: 1639 1.46 - 1.58: 3520 1.58 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 7485 Sorted by residual: bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" CB VAL A 334 " pdb=" CG1 VAL A 334 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.88e-01 bond pdb=" C GLY A 412 " pdb=" N ASN A 413 " ideal model delta sigma weight residual 1.332 1.321 0.012 1.40e-02 5.10e+03 6.80e-01 bond pdb=" CA PHE B 14 " pdb=" C PHE B 14 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.34e-02 5.57e+03 4.15e-01 bond pdb=" N PRO A 333 " pdb=" CA PRO A 333 " ideal model delta sigma weight residual 1.468 1.475 -0.007 1.20e-02 6.94e+03 3.84e-01 ... (remaining 7480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 9551 0.88 - 1.76: 464 1.76 - 2.64: 65 2.64 - 3.52: 21 3.52 - 4.40: 12 Bond angle restraints: 10113 Sorted by residual: angle pdb=" N ASN B 446 " pdb=" CA ASN B 446 " pdb=" CB ASN B 446 " ideal model delta sigma weight residual 110.07 112.31 -2.24 1.45e+00 4.76e-01 2.38e+00 angle pdb=" N ARG B 24 " pdb=" CA ARG B 24 " pdb=" CB ARG B 24 " ideal model delta sigma weight residual 110.91 108.52 2.39 1.58e+00 4.01e-01 2.28e+00 angle pdb=" C GLN B 205 " pdb=" N PHE B 206 " pdb=" CA PHE B 206 " ideal model delta sigma weight residual 120.82 123.01 -2.19 1.50e+00 4.44e-01 2.13e+00 angle pdb=" C ALA B 212 " pdb=" N ARG B 213 " pdb=" CA ARG B 213 " ideal model delta sigma weight residual 122.27 119.63 2.64 1.85e+00 2.92e-01 2.03e+00 angle pdb=" N THR A 389 " pdb=" CA THR A 389 " pdb=" C THR A 389 " ideal model delta sigma weight residual 110.80 113.77 -2.97 2.13e+00 2.20e-01 1.95e+00 ... (remaining 10108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 4028 17.17 - 34.35: 375 34.35 - 51.52: 60 51.52 - 68.69: 12 68.69 - 85.87: 5 Dihedral angle restraints: 4480 sinusoidal: 1856 harmonic: 2624 Sorted by residual: dihedral pdb=" CA LEU B 36 " pdb=" C LEU B 36 " pdb=" N TYR B 37 " pdb=" CA TYR B 37 " ideal model delta harmonic sigma weight residual -180.00 -161.97 -18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA PHE B 304 " pdb=" C PHE B 304 " pdb=" N LEU B 305 " pdb=" CA LEU B 305 " ideal model delta harmonic sigma weight residual 180.00 162.62 17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA LYS B 392 " pdb=" C LYS B 392 " pdb=" N PRO B 393 " pdb=" CA PRO B 393 " ideal model delta harmonic sigma weight residual -180.00 -163.28 -16.72 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 4477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 665 0.027 - 0.055: 271 0.055 - 0.082: 72 0.082 - 0.110: 52 0.110 - 0.137: 26 Chirality restraints: 1086 Sorted by residual: chirality pdb=" CA ILE A 418 " pdb=" N ILE A 418 " pdb=" C ILE A 418 " pdb=" CB ILE A 418 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE A 5 " pdb=" N ILE A 5 " pdb=" C ILE A 5 " pdb=" CB ILE A 5 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA VAL A 140 " pdb=" N VAL A 140 " pdb=" C VAL A 140 " pdb=" CB VAL A 140 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1083 not shown) Planarity restraints: 1279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 11 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO A 12 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 12 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 12 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 332 " 0.009 2.00e-02 2.50e+03 1.23e-02 2.67e+00 pdb=" CG PHE A 332 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 332 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 332 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 332 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 332 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 332 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 418 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A 419 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 419 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 419 " 0.020 5.00e-02 4.00e+02 ... (remaining 1276 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 50 2.51 - 3.11: 5542 3.11 - 3.70: 10926 3.70 - 4.30: 16234 4.30 - 4.90: 27214 Nonbonded interactions: 59966 Sorted by model distance: nonbonded pdb=" OH TYR A 154 " pdb=" OD2 ASP B 25 " model vdw 1.911 3.040 nonbonded pdb=" O TRP B 269 " pdb=" OH TYR B 467 " model vdw 2.183 3.040 nonbonded pdb=" O PHE B 365 " pdb=" NZ LYS B 447 " model vdw 2.201 3.120 nonbonded pdb=" OD1 ASN A 270 " pdb=" OG SER A 327 " model vdw 2.206 3.040 nonbonded pdb=" OD2 ASP B 22 " pdb=" NZ LYS B 428 " model vdw 2.230 3.120 ... (remaining 59961 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: 8.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.350 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 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 : 0.003 0.032 7485 Z= 0.114 Angle : 0.459 4.396 10113 Z= 0.243 Chirality : 0.040 0.137 1086 Planarity : 0.003 0.042 1279 Dihedral : 13.443 85.868 2784 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.93 (0.28), residues: 885 helix: 0.94 (0.32), residues: 300 sheet: -0.92 (0.43), residues: 158 loop : -1.65 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 240 TYR 0.010 0.001 TYR B 115 PHE 0.026 0.001 PHE A 332 TRP 0.007 0.001 TRP B 269 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7485) covalent geometry : angle 0.45894 (10113) hydrogen bonds : bond 0.17225 ( 255) hydrogen bonds : angle 7.81378 ( 702) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1162 time to fit residues: 15.8945 Evaluate side-chains 89 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.0470 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.0470 chunk 45 optimal weight: 0.1980 chunk 74 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN B 322 ASN B 349 GLN B 446 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.203160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.169915 restraints weight = 7893.236| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 2.02 r_work: 0.3912 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7485 Z= 0.154 Angle : 0.532 7.282 10113 Z= 0.280 Chirality : 0.042 0.156 1086 Planarity : 0.004 0.033 1279 Dihedral : 4.235 18.604 962 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.88 % Allowed : 7.03 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.73 (0.28), residues: 885 helix: 1.17 (0.31), residues: 304 sheet: -1.21 (0.42), residues: 163 loop : -1.43 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 240 TYR 0.007 0.001 TYR A 154 PHE 0.020 0.002 PHE A 332 TRP 0.011 0.001 TRP B 370 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 7485) covalent geometry : angle 0.53200 (10113) hydrogen bonds : bond 0.04522 ( 255) hydrogen bonds : angle 5.69282 ( 702) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.313 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 99 average time/residue: 0.1073 time to fit residues: 13.8923 Evaluate side-chains 98 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 380 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.200719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.164100 restraints weight = 7915.106| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.19 r_work: 0.3857 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7485 Z= 0.157 Angle : 0.528 7.033 10113 Z= 0.276 Chirality : 0.042 0.138 1086 Planarity : 0.004 0.036 1279 Dihedral : 4.327 18.340 962 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.51 % Allowed : 10.92 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.74 (0.28), residues: 885 helix: 1.12 (0.30), residues: 304 sheet: -1.22 (0.42), residues: 161 loop : -1.40 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 240 TYR 0.008 0.001 TYR A 293 PHE 0.024 0.002 PHE A 342 TRP 0.011 0.001 TRP B 370 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 7485) covalent geometry : angle 0.52774 (10113) hydrogen bonds : bond 0.04076 ( 255) hydrogen bonds : angle 5.39762 ( 702) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.316 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 97 average time/residue: 0.1098 time to fit residues: 13.8044 Evaluate side-chains 94 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 380 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 4.9990 chunk 24 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.202402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.168287 restraints weight = 7953.224| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 2.15 r_work: 0.3905 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7485 Z= 0.122 Angle : 0.494 6.608 10113 Z= 0.259 Chirality : 0.041 0.139 1086 Planarity : 0.004 0.037 1279 Dihedral : 4.210 18.246 962 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.13 % Allowed : 12.42 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.61 (0.28), residues: 885 helix: 1.27 (0.31), residues: 304 sheet: -1.23 (0.42), residues: 161 loop : -1.32 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 240 TYR 0.008 0.001 TYR A 293 PHE 0.023 0.002 PHE A 342 TRP 0.012 0.001 TRP B 320 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7485) covalent geometry : angle 0.49397 (10113) hydrogen bonds : bond 0.03630 ( 255) hydrogen bonds : angle 5.17497 ( 702) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.295 Fit side-chains REVERT: B 39 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7983 (mt) outliers start: 17 outliers final: 11 residues processed: 102 average time/residue: 0.0940 time to fit residues: 12.8103 Evaluate side-chains 98 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 380 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.198093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.160533 restraints weight = 8049.605| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.23 r_work: 0.3822 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7485 Z= 0.203 Angle : 0.576 8.150 10113 Z= 0.299 Chirality : 0.043 0.175 1086 Planarity : 0.004 0.039 1279 Dihedral : 4.493 18.121 962 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.89 % Allowed : 12.92 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.99 (0.27), residues: 885 helix: 0.87 (0.30), residues: 309 sheet: -1.34 (0.41), residues: 157 loop : -1.54 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 240 TYR 0.008 0.001 TYR A 154 PHE 0.024 0.002 PHE A 342 TRP 0.013 0.002 TRP B 320 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00503 ( 7485) covalent geometry : angle 0.57594 (10113) hydrogen bonds : bond 0.04243 ( 255) hydrogen bonds : angle 5.33179 ( 702) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7078 (tp30) cc_final: 0.6802 (tp30) REVERT: A 394 GLU cc_start: 0.6374 (mt-10) cc_final: 0.5999 (mm-30) outliers start: 23 outliers final: 16 residues processed: 102 average time/residue: 0.0994 time to fit residues: 13.2347 Evaluate side-chains 102 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 474 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 12 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 50 optimal weight: 0.0870 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 42 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.203287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.167283 restraints weight = 7988.598| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.12 r_work: 0.3893 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7485 Z= 0.117 Angle : 0.505 9.327 10113 Z= 0.261 Chirality : 0.041 0.223 1086 Planarity : 0.004 0.038 1279 Dihedral : 4.233 18.490 962 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.63 % Allowed : 13.93 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.77 (0.28), residues: 885 helix: 1.18 (0.31), residues: 310 sheet: -1.49 (0.39), residues: 169 loop : -1.38 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 240 TYR 0.006 0.001 TYR A 293 PHE 0.017 0.001 PHE A 342 TRP 0.016 0.001 TRP B 320 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7485) covalent geometry : angle 0.50505 (10113) hydrogen bonds : bond 0.03440 ( 255) hydrogen bonds : angle 5.03131 ( 702) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.304 Fit side-chains REVERT: A 189 GLU cc_start: 0.7114 (tp30) cc_final: 0.6829 (tp30) REVERT: A 394 GLU cc_start: 0.6348 (mt-10) cc_final: 0.6088 (mm-30) REVERT: B 134 GLU cc_start: 0.6081 (OUTLIER) cc_final: 0.5671 (pm20) REVERT: B 285 TYR cc_start: 0.6606 (t80) cc_final: 0.5305 (t80) outliers start: 21 outliers final: 14 residues processed: 100 average time/residue: 0.0995 time to fit residues: 13.3387 Evaluate side-chains 100 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 426 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 38 optimal weight: 0.4980 chunk 79 optimal weight: 0.5980 chunk 4 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.203050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.165235 restraints weight = 7926.177| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.30 r_work: 0.3878 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7485 Z= 0.099 Angle : 0.470 7.627 10113 Z= 0.246 Chirality : 0.040 0.204 1086 Planarity : 0.003 0.032 1279 Dihedral : 4.066 17.443 962 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.65 % Favored : 94.24 % Rotamer: Outliers : 2.51 % Allowed : 14.93 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.60 (0.28), residues: 885 helix: 1.35 (0.31), residues: 311 sheet: -1.49 (0.40), residues: 160 loop : -1.30 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 240 TYR 0.006 0.001 TYR A 154 PHE 0.014 0.001 PHE A 342 TRP 0.019 0.001 TRP B 320 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 7485) covalent geometry : angle 0.47016 (10113) hydrogen bonds : bond 0.03213 ( 255) hydrogen bonds : angle 4.82934 ( 702) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.282 Fit side-chains REVERT: A 394 GLU cc_start: 0.6235 (mt-10) cc_final: 0.5890 (mm-30) REVERT: B 134 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5544 (pm20) REVERT: B 285 TYR cc_start: 0.6692 (t80) cc_final: 0.5308 (t80) REVERT: B 503 PHE cc_start: 0.7342 (OUTLIER) cc_final: 0.6613 (m-80) outliers start: 20 outliers final: 14 residues processed: 103 average time/residue: 0.0887 time to fit residues: 12.2508 Evaluate side-chains 104 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 503 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 18 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.201824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.168476 restraints weight = 7950.585| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.01 r_work: 0.3904 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7485 Z= 0.146 Angle : 0.515 8.064 10113 Z= 0.268 Chirality : 0.042 0.199 1086 Planarity : 0.004 0.034 1279 Dihedral : 4.212 17.749 962 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.51 % Allowed : 15.43 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.74 (0.28), residues: 885 helix: 1.14 (0.30), residues: 311 sheet: -1.53 (0.39), residues: 171 loop : -1.28 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 240 TYR 0.008 0.001 TYR A 154 PHE 0.019 0.002 PHE A 342 TRP 0.021 0.002 TRP B 320 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 7485) covalent geometry : angle 0.51489 (10113) hydrogen bonds : bond 0.03583 ( 255) hydrogen bonds : angle 4.99575 ( 702) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.292 Fit side-chains REVERT: A 189 GLU cc_start: 0.7016 (tp30) cc_final: 0.6779 (tp30) REVERT: A 285 TYR cc_start: 0.6605 (t80) cc_final: 0.6312 (t80) REVERT: B 134 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5626 (pm20) REVERT: B 285 TYR cc_start: 0.6934 (t80) cc_final: 0.5536 (t80) REVERT: B 503 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.6777 (m-80) outliers start: 20 outliers final: 16 residues processed: 98 average time/residue: 0.1048 time to fit residues: 13.4285 Evaluate side-chains 105 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 503 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 13 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 15 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 68 optimal weight: 0.0870 chunk 17 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.204064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.170620 restraints weight = 7809.729| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.05 r_work: 0.3940 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3803 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7485 Z= 0.104 Angle : 0.493 11.435 10113 Z= 0.254 Chirality : 0.040 0.193 1086 Planarity : 0.003 0.032 1279 Dihedral : 4.087 17.710 962 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.51 % Allowed : 15.68 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.59 (0.28), residues: 885 helix: 1.36 (0.31), residues: 311 sheet: -1.58 (0.40), residues: 162 loop : -1.24 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 240 TYR 0.007 0.001 TYR A 154 PHE 0.015 0.001 PHE A 342 TRP 0.023 0.001 TRP B 320 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 7485) covalent geometry : angle 0.49331 (10113) hydrogen bonds : bond 0.03182 ( 255) hydrogen bonds : angle 4.81562 ( 702) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.287 Fit side-chains REVERT: A 189 GLU cc_start: 0.7028 (tp30) cc_final: 0.6777 (tp30) REVERT: A 285 TYR cc_start: 0.6514 (t80) cc_final: 0.6058 (t80) REVERT: A 395 MET cc_start: 0.5619 (mmm) cc_final: 0.4799 (mmm) REVERT: B 134 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5671 (pm20) REVERT: B 285 TYR cc_start: 0.6841 (t80) cc_final: 0.5496 (t80) REVERT: B 485 LYS cc_start: 0.7132 (tppt) cc_final: 0.6909 (tptp) REVERT: B 503 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6682 (m-80) outliers start: 20 outliers final: 14 residues processed: 98 average time/residue: 0.0889 time to fit residues: 11.7417 Evaluate side-chains 104 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 503 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 0.0010 chunk 78 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.204615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.168180 restraints weight = 7885.020| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.13 r_work: 0.3898 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7485 Z= 0.120 Angle : 0.504 10.344 10113 Z= 0.259 Chirality : 0.041 0.187 1086 Planarity : 0.004 0.036 1279 Dihedral : 4.113 17.446 962 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.26 % Allowed : 16.31 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.63 (0.28), residues: 885 helix: 1.25 (0.31), residues: 311 sheet: -1.47 (0.39), residues: 169 loop : -1.24 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 240 TYR 0.009 0.001 TYR A 154 PHE 0.015 0.001 PHE A 342 TRP 0.025 0.001 TRP B 320 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7485) covalent geometry : angle 0.50439 (10113) hydrogen bonds : bond 0.03324 ( 255) hydrogen bonds : angle 4.82102 ( 702) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.294 Fit side-chains REVERT: A 184 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7125 (mt-10) REVERT: A 189 GLU cc_start: 0.7044 (tp30) cc_final: 0.6781 (tp30) REVERT: A 285 TYR cc_start: 0.6446 (t80) cc_final: 0.5966 (t80) REVERT: A 395 MET cc_start: 0.5719 (mmm) cc_final: 0.4826 (mmm) REVERT: B 134 GLU cc_start: 0.6135 (OUTLIER) cc_final: 0.5631 (pm20) REVERT: B 285 TYR cc_start: 0.6934 (t80) cc_final: 0.5579 (t80) REVERT: B 485 LYS cc_start: 0.7145 (tppt) cc_final: 0.6926 (tptp) REVERT: B 503 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6711 (m-80) outliers start: 18 outliers final: 14 residues processed: 97 average time/residue: 0.0985 time to fit residues: 12.8737 Evaluate side-chains 104 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 503 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 11 optimal weight: 0.0000 chunk 67 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 20 optimal weight: 0.0010 chunk 1 optimal weight: 0.9980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.206557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.168156 restraints weight = 7920.827| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.39 r_work: 0.3875 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7485 Z= 0.105 Angle : 0.493 10.042 10113 Z= 0.254 Chirality : 0.040 0.184 1086 Planarity : 0.004 0.039 1279 Dihedral : 4.058 17.554 962 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.20 % Favored : 94.69 % Rotamer: Outliers : 2.38 % Allowed : 16.19 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.56 (0.28), residues: 885 helix: 1.35 (0.31), residues: 310 sheet: -1.44 (0.39), residues: 169 loop : -1.23 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 240 TYR 0.008 0.001 TYR A 154 PHE 0.013 0.001 PHE A 342 TRP 0.023 0.001 TRP B 320 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 7485) covalent geometry : angle 0.49330 (10113) hydrogen bonds : bond 0.03163 ( 255) hydrogen bonds : angle 4.75742 ( 702) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1893.42 seconds wall clock time: 33 minutes 12.46 seconds (1992.46 seconds total)