Starting phenix.real_space_refine on Fri Jun 6 05:55:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fex_29033/06_2025/8fex_29033_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fex_29033/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fex_29033/06_2025/8fex_29033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fex_29033/06_2025/8fex_29033.map" model { file = "/net/cci-nas-00/data/ceres_data/8fex_29033/06_2025/8fex_29033_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fex_29033/06_2025/8fex_29033_neut.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.34, per 1000 atoms: 0.87 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: 1.95 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.83 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: 1.99 Time building geometry restraints manager: 2.20 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: 34.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.220 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.670 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (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 TRP 0.007 0.001 TRP B 269 HIS 0.005 0.001 HIS B 207 PHE 0.026 0.001 PHE A 332 TYR 0.010 0.001 TYR B 115 ARG 0.003 0.000 ARG A 240 Details of bonding type rmsd hydrogen bonds : bond 0.17225 ( 255) hydrogen bonds : angle 7.81378 ( 702) covalent geometry : bond 0.00257 ( 7485) covalent geometry : angle 0.45894 (10113) *********************** 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 : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2596 time to fit residues: 35.8247 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 : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 68 optimal weight: 0.0870 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 0.0970 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.205275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.171943 restraints weight = 7756.529| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 2.11 r_work: 0.3947 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.1209 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= 0.117 Angle : 0.501 6.997 10113 Z= 0.265 Chirality : 0.041 0.142 1086 Planarity : 0.004 0.032 1279 Dihedral : 4.163 18.478 962 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.88 % Allowed : 6.90 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.28), residues: 885 helix: 1.35 (0.31), residues: 304 sheet: -1.15 (0.42), residues: 161 loop : -1.32 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 370 HIS 0.006 0.001 HIS B 207 PHE 0.020 0.002 PHE A 332 TYR 0.008 0.001 TYR B 115 ARG 0.006 0.001 ARG A 240 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 255) hydrogen bonds : angle 5.52501 ( 702) covalent geometry : bond 0.00267 ( 7485) covalent geometry : angle 0.50100 (10113) *********************** 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 109 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 1.077 Fit side-chains revert: symmetry clash REVERT: A 313 LYS cc_start: 0.7600 (ptpt) cc_final: 0.7129 (tttt) outliers start: 7 outliers final: 7 residues processed: 104 average time/residue: 0.3262 time to fit residues: 45.6343 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 : 1.876 ------------------------------------------------------------------------------- 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 80 optimal weight: 0.0980 chunk 83 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN B 446 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.203668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.170732 restraints weight = 7910.766| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.01 r_work: 0.3924 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7485 Z= 0.136 Angle : 0.497 6.790 10113 Z= 0.261 Chirality : 0.041 0.133 1086 Planarity : 0.004 0.035 1279 Dihedral : 4.176 17.953 962 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.38 % Allowed : 10.54 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.28), residues: 885 helix: 1.28 (0.31), residues: 304 sheet: -1.10 (0.43), residues: 161 loop : -1.34 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 370 HIS 0.007 0.001 HIS B 207 PHE 0.019 0.002 PHE B 503 TYR 0.009 0.001 TYR A 293 ARG 0.008 0.001 ARG A 240 Details of bonding type rmsd hydrogen bonds : bond 0.03897 ( 255) hydrogen bonds : angle 5.31248 ( 702) covalent geometry : bond 0.00327 ( 7485) covalent geometry : angle 0.49683 (10113) *********************** 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: 11 poor density : 93 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 313 LYS cc_start: 0.7596 (ptpt) cc_final: 0.7156 (tttt) outliers start: 11 outliers final: 9 residues processed: 98 average time/residue: 0.2436 time to fit residues: 30.9273 Evaluate side-chains 99 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 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 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 72 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 0.0970 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.4381 r_free = 0.4381 target = 0.204238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.169890 restraints weight = 7873.906| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.17 r_work: 0.3932 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7485 Z= 0.116 Angle : 0.478 7.432 10113 Z= 0.251 Chirality : 0.040 0.140 1086 Planarity : 0.003 0.038 1279 Dihedral : 4.112 18.145 962 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.65 % Favored : 94.24 % Rotamer: Outliers : 1.88 % Allowed : 12.05 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.28), residues: 885 helix: 1.27 (0.31), residues: 309 sheet: -1.18 (0.42), residues: 161 loop : -1.36 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 320 HIS 0.006 0.001 HIS B 207 PHE 0.024 0.002 PHE A 342 TYR 0.007 0.001 TYR A 293 ARG 0.007 0.000 ARG A 240 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 255) hydrogen bonds : angle 5.10972 ( 702) covalent geometry : bond 0.00274 ( 7485) covalent geometry : angle 0.47778 (10113) *********************** 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 105 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: B 39 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7902 (mt) outliers start: 15 outliers final: 9 residues processed: 99 average time/residue: 0.2053 time to fit residues: 27.6864 Evaluate side-chains 95 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 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 44 ILE 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 68 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.4330 r_free = 0.4330 target = 0.199237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.162187 restraints weight = 7892.695| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.19 r_work: 0.3851 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7485 Z= 0.184 Angle : 0.549 8.050 10113 Z= 0.286 Chirality : 0.043 0.166 1086 Planarity : 0.004 0.038 1279 Dihedral : 4.373 17.940 962 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.14 % Allowed : 12.05 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.28), residues: 885 helix: 0.94 (0.30), residues: 310 sheet: -1.34 (0.41), residues: 169 loop : -1.51 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 320 HIS 0.008 0.001 HIS B 207 PHE 0.023 0.002 PHE A 342 TYR 0.008 0.001 TYR B 505 ARG 0.008 0.000 ARG A 240 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 255) hydrogen bonds : angle 5.24829 ( 702) covalent geometry : bond 0.00454 ( 7485) covalent geometry : angle 0.54915 (10113) *********************** 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 113 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.873 Fit side-chains REVERT: A 189 GLU cc_start: 0.7010 (tp30) cc_final: 0.6712 (tp30) REVERT: B 39 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8066 (mt) REVERT: B 134 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.5581 (pm20) REVERT: B 343 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6807 (mm) REVERT: B 503 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.6827 (m-80) outliers start: 25 outliers final: 15 residues processed: 104 average time/residue: 0.2294 time to fit residues: 31.5791 Evaluate side-chains 104 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 39 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 274 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 503 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 5 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 50 optimal weight: 0.0980 chunk 84 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.202288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.167971 restraints weight = 7855.680| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 2.15 r_work: 0.3911 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7485 Z= 0.124 Angle : 0.496 8.972 10113 Z= 0.259 Chirality : 0.041 0.143 1086 Planarity : 0.004 0.039 1279 Dihedral : 4.225 18.500 962 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.76 % Allowed : 13.30 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.28), residues: 885 helix: 1.17 (0.31), residues: 309 sheet: -1.41 (0.40), residues: 169 loop : -1.42 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 320 HIS 0.007 0.001 HIS B 207 PHE 0.018 0.002 PHE A 342 TYR 0.006 0.001 TYR A 154 ARG 0.009 0.000 ARG A 240 Details of bonding type rmsd hydrogen bonds : bond 0.03468 ( 255) hydrogen bonds : angle 5.04974 ( 702) covalent geometry : bond 0.00297 ( 7485) covalent geometry : angle 0.49617 (10113) *********************** 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 112 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.917 Fit side-chains REVERT: A 394 GLU cc_start: 0.6359 (mt-10) cc_final: 0.6053 (mm-30) REVERT: B 39 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7988 (mt) REVERT: B 134 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5633 (pm20) REVERT: B 285 TYR cc_start: 0.6805 (t80) cc_final: 0.5430 (t80) REVERT: B 485 LYS cc_start: 0.7093 (tppt) cc_final: 0.6854 (tptp) REVERT: B 503 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.6852 (m-80) outliers start: 22 outliers final: 11 residues processed: 104 average time/residue: 0.2587 time to fit residues: 36.2285 Evaluate side-chains 100 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 39 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 47 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 69 optimal weight: 0.0870 chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 = 0.4379 r_free = 0.4379 target = 0.203898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.170386 restraints weight = 7801.672| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 2.10 r_work: 0.3939 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7485 Z= 0.103 Angle : 0.470 7.526 10113 Z= 0.246 Chirality : 0.040 0.145 1086 Planarity : 0.003 0.039 1279 Dihedral : 4.075 17.632 962 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.88 % Favored : 94.01 % Rotamer: Outliers : 2.51 % Allowed : 14.30 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.28), residues: 885 helix: 1.32 (0.31), residues: 310 sheet: -1.36 (0.40), residues: 169 loop : -1.32 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 320 HIS 0.007 0.001 HIS B 207 PHE 0.015 0.001 PHE A 342 TYR 0.006 0.001 TYR A 154 ARG 0.009 0.000 ARG A 240 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 255) hydrogen bonds : angle 4.88129 ( 702) covalent geometry : bond 0.00239 ( 7485) covalent geometry : angle 0.46964 (10113) *********************** 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 : 1.115 Fit side-chains REVERT: A 189 GLU cc_start: 0.6995 (tp30) cc_final: 0.6750 (tp30) REVERT: A 285 TYR cc_start: 0.6688 (t80) cc_final: 0.6382 (t80) REVERT: B 39 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7842 (mt) REVERT: B 134 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.5663 (pm20) REVERT: B 285 TYR cc_start: 0.6842 (t80) cc_final: 0.5518 (t80) REVERT: B 503 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6844 (m-80) outliers start: 20 outliers final: 15 residues processed: 103 average time/residue: 0.2564 time to fit residues: 35.6657 Evaluate side-chains 107 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 1.678 ------------------------------------------------------------------------------- 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 389 THR 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 39 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 317 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 69 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4365 r_free = 0.4365 target = 0.202453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.168531 restraints weight = 7847.374| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.16 r_work: 0.3915 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7485 Z= 0.126 Angle : 0.488 7.996 10113 Z= 0.255 Chirality : 0.041 0.152 1086 Planarity : 0.004 0.033 1279 Dihedral : 4.115 17.859 962 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.26 % Allowed : 15.43 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.28), residues: 885 helix: 1.26 (0.31), residues: 310 sheet: -1.46 (0.39), residues: 171 loop : -1.27 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 320 HIS 0.007 0.001 HIS B 207 PHE 0.016 0.002 PHE A 342 TYR 0.008 0.001 TYR A 154 ARG 0.007 0.000 ARG A 240 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 255) hydrogen bonds : angle 4.87980 ( 702) covalent geometry : bond 0.00306 ( 7485) covalent geometry : angle 0.48827 (10113) *********************** 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: 18 poor density : 91 time to evaluate : 0.667 Fit side-chains REVERT: A 189 GLU cc_start: 0.7054 (tp30) cc_final: 0.6736 (tp30) REVERT: A 285 TYR cc_start: 0.6628 (t80) cc_final: 0.6297 (t80) REVERT: B 39 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7925 (mt) REVERT: B 134 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5660 (pm20) REVERT: B 285 TYR cc_start: 0.6846 (t80) cc_final: 0.5482 (t80) REVERT: B 485 LYS cc_start: 0.7139 (tppt) cc_final: 0.6881 (tptp) REVERT: B 503 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6901 (m-80) outliers start: 18 outliers final: 15 residues processed: 101 average time/residue: 0.2563 time to fit residues: 33.7523 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 : 0.869 ------------------------------------------------------------------------------- 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 389 THR 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 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 317 VAL 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 66 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 0.0570 chunk 82 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 41 optimal weight: 0.0270 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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 = 0.4383 r_free = 0.4383 target = 0.204553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.171241 restraints weight = 7866.099| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 2.08 r_work: 0.3945 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3804 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2095 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 : 0.487 11.356 10113 Z= 0.251 Chirality : 0.040 0.134 1086 Planarity : 0.003 0.032 1279 Dihedral : 4.051 17.637 962 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.54 % Favored : 94.35 % Rotamer: Outliers : 2.38 % Allowed : 15.43 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.28), residues: 885 helix: 1.37 (0.31), residues: 309 sheet: -1.43 (0.39), residues: 171 loop : -1.25 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 320 HIS 0.006 0.001 HIS B 207 PHE 0.014 0.001 PHE A 342 TYR 0.006 0.001 TYR A 154 ARG 0.006 0.000 ARG A 240 Details of bonding type rmsd hydrogen bonds : bond 0.03125 ( 255) hydrogen bonds : angle 4.84069 ( 702) covalent geometry : bond 0.00243 ( 7485) covalent geometry : angle 0.48739 (10113) *********************** 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 110 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.781 Fit side-chains REVERT: A 189 GLU cc_start: 0.7083 (tp30) cc_final: 0.6777 (tp30) REVERT: A 285 TYR cc_start: 0.6414 (t80) cc_final: 0.5977 (t80) REVERT: A 328 LYS cc_start: 0.7875 (tttt) cc_final: 0.7460 (ttpt) REVERT: A 395 MET cc_start: 0.5600 (mmm) cc_final: 0.4730 (mmm) REVERT: B 39 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7778 (mt) REVERT: B 134 GLU cc_start: 0.6203 (OUTLIER) cc_final: 0.5649 (pm20) REVERT: B 285 TYR cc_start: 0.6868 (t80) cc_final: 0.5529 (t80) REVERT: B 485 LYS cc_start: 0.7134 (tppt) cc_final: 0.6864 (tptp) REVERT: B 503 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.6837 (m-80) outliers start: 19 outliers final: 13 residues processed: 102 average time/residue: 0.3245 time to fit residues: 44.9840 Evaluate side-chains 103 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 389 THR 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 39 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 317 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 81 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 chunk 30 optimal weight: 0.2980 chunk 87 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4348 r_free = 0.4348 target = 0.201629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.168046 restraints weight = 7985.482| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.02 r_work: 0.3887 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2045 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= 0.160 Angle : 0.542 10.386 10113 Z= 0.278 Chirality : 0.042 0.142 1086 Planarity : 0.004 0.035 1279 Dihedral : 4.257 17.691 962 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.26 % Allowed : 15.43 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.28), residues: 885 helix: 1.17 (0.30), residues: 308 sheet: -1.50 (0.40), residues: 171 loop : -1.35 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 320 HIS 0.008 0.001 HIS B 207 PHE 0.017 0.002 PHE B 503 TYR 0.009 0.001 TYR A 154 ARG 0.006 0.000 ARG A 240 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 255) hydrogen bonds : angle 4.96052 ( 702) covalent geometry : bond 0.00393 ( 7485) covalent geometry : angle 0.54188 (10113) ********************** 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 108 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 1.352 Fit side-chains REVERT: A 189 GLU cc_start: 0.7101 (tp30) cc_final: 0.6769 (tp30) REVERT: A 395 MET cc_start: 0.5795 (mmm) cc_final: 0.4923 (mmm) REVERT: B 39 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.8000 (mt) REVERT: B 134 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5692 (pm20) REVERT: B 285 TYR cc_start: 0.6902 (t80) cc_final: 0.5538 (t80) REVERT: B 295 ARG cc_start: 0.7223 (mmm-85) cc_final: 0.6616 (mtp85) REVERT: B 503 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6945 (m-80) outliers start: 18 outliers final: 14 residues processed: 101 average time/residue: 0.2815 time to fit residues: 39.0789 Evaluate side-chains 106 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 39 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 24 optimal weight: 3.9990 chunk 56 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 72 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.206620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.168305 restraints weight = 7791.536| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.36 r_work: 0.3888 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7485 Z= 0.105 Angle : 0.505 10.027 10113 Z= 0.258 Chirality : 0.041 0.264 1086 Planarity : 0.003 0.032 1279 Dihedral : 4.075 18.060 962 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.42 % Favored : 94.46 % Rotamer: Outliers : 2.26 % Allowed : 15.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.28), residues: 885 helix: 1.35 (0.31), residues: 309 sheet: -1.54 (0.40), residues: 162 loop : -1.29 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 320 HIS 0.007 0.001 HIS B 207 PHE 0.013 0.001 PHE B 503 TYR 0.007 0.001 TYR A 154 ARG 0.006 0.000 ARG A 240 Details of bonding type rmsd hydrogen bonds : bond 0.03176 ( 255) hydrogen bonds : angle 4.86899 ( 702) covalent geometry : bond 0.00247 ( 7485) covalent geometry : angle 0.50478 (10113) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6024.91 seconds wall clock time: 110 minutes 47.78 seconds (6647.78 seconds total)