Starting phenix.real_space_refine on Tue Mar 11 14:30:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bw8_30230/03_2025/7bw8_30230.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bw8_30230/03_2025/7bw8_30230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bw8_30230/03_2025/7bw8_30230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bw8_30230/03_2025/7bw8_30230.map" model { file = "/net/cci-nas-00/data/ceres_data/7bw8_30230/03_2025/7bw8_30230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bw8_30230/03_2025/7bw8_30230.cif" } resolution = 3.8 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= 0.004 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 46 5.16 5 C 3847 2.51 5 N 1026 2.21 5 O 1102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6021 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4469 Classifications: {'peptide': 551} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 525} Chain breaks: 3 Chain: "C" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1176 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain breaks: 2 Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Time building chain proxies: 4.00, per 1000 atoms: 0.66 Number of scatterers: 6021 At special positions: 0 Unit cell: (83.57, 94.53, 108.23, 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 46 16.00 O 1102 8.00 N 1026 7.00 C 3847 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.05 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.02 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.01 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.01 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=1.71 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.02 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 62 " distance=2.04 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 66 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 872.6 milliseconds 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1398 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 11 sheets defined 15.2% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 removed outlier: 3.854A pdb=" N LEU A 20 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.625A pdb=" N ASP A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.861A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.656A pdb=" N GLY A 317 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 435 through 447 removed outlier: 4.108A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 removed outlier: 3.553A pdb=" N LEU A 500 " --> pdb=" O PHE A 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 697 Processing helix chain 'C' and resid 697 through 713 removed outlier: 4.209A pdb=" N LYS C 703 " --> pdb=" O SER C 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 19 removed outlier: 3.874A pdb=" N CYS D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 69 through 74 removed outlier: 3.944A pdb=" N ASN D 73 " --> pdb=" O TYR D 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 6.128A pdb=" N ILE A 13 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N MET A 38 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A 63 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N MET A 98 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR A 67 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 removed outlier: 3.625A pdb=" N ILE A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A 82 " --> pdb=" O ASN A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA4, first strand: chain 'A' and resid 278 through 279 Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA6, first strand: chain 'A' and resid 335 through 336 removed outlier: 3.575A pdb=" N ILE A 336 " --> pdb=" O GLU A 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AA8, first strand: chain 'A' and resid 474 through 479 removed outlier: 6.233A pdb=" N PHE A 475 " --> pdb=" O GLU A 490 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU A 490 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.750A pdb=" N THR A 530 " --> pdb=" O TYR A 507 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR A 507 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR A 562 " --> pdb=" O VAL A 588 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 588 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 566 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASP A 584 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR A 568 " --> pdb=" O LYS A 582 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LYS A 582 " --> pdb=" O THR A 568 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 485 through 486 removed outlier: 3.622A pdb=" N ILE C 485 " --> pdb=" O MET C 553 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 531 through 534 removed outlier: 3.574A pdb=" N VAL C 532 " --> pdb=" O LEU C 505 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR C 560 " --> pdb=" O THR C 590 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL C 566 " --> pdb=" O ASP C 584 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASP C 584 " --> pdb=" O VAL C 566 " (cutoff:3.500A) 101 hydrogen bonds defined for protein. 258 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: 1.45 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1478 1.33 - 1.46: 1574 1.46 - 1.58: 3063 1.58 - 1.71: 0 1.71 - 1.83: 57 Bond restraints: 6172 Sorted by residual: bond pdb=" N GLN A 589 " pdb=" CA GLN A 589 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.27e-02 6.20e+03 1.08e+01 bond pdb=" C PRO C 536 " pdb=" N PRO C 537 " ideal model delta sigma weight residual 1.335 1.307 0.028 8.70e-03 1.32e+04 1.04e+01 bond pdb=" N TYR A 477 " pdb=" CA TYR A 477 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.25e-02 6.40e+03 7.83e+00 bond pdb=" N VAL D 12 " pdb=" CA VAL D 12 " ideal model delta sigma weight residual 1.460 1.492 -0.033 1.21e-02 6.83e+03 7.33e+00 bond pdb=" N ARG A 252 " pdb=" CA ARG A 252 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.27e-02 6.20e+03 7.20e+00 ... (remaining 6167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 7700 2.46 - 4.92: 584 4.92 - 7.38: 69 7.38 - 9.84: 7 9.84 - 12.29: 3 Bond angle restraints: 8363 Sorted by residual: angle pdb=" N VAL A 445 " pdb=" CA VAL A 445 " pdb=" C VAL A 445 " ideal model delta sigma weight residual 112.29 108.64 3.65 9.40e-01 1.13e+00 1.51e+01 angle pdb=" N GLY C 555 " pdb=" CA GLY C 555 " pdb=" C GLY C 555 " ideal model delta sigma weight residual 113.18 122.28 -9.10 2.37e+00 1.78e-01 1.47e+01 angle pdb=" CA TYR D 16 " pdb=" CB TYR D 16 " pdb=" CG TYR D 16 " ideal model delta sigma weight residual 113.90 107.05 6.85 1.80e+00 3.09e-01 1.45e+01 angle pdb=" CA TRP C 559 " pdb=" C TRP C 559 " pdb=" O TRP C 559 " ideal model delta sigma weight residual 122.27 117.87 4.40 1.16e+00 7.43e-01 1.44e+01 angle pdb=" C THR C 560 " pdb=" N GLN C 561 " pdb=" CA GLN C 561 " ideal model delta sigma weight residual 120.87 126.15 -5.28 1.42e+00 4.96e-01 1.38e+01 ... (remaining 8358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3109 17.96 - 35.92: 482 35.92 - 53.88: 106 53.88 - 71.84: 13 71.84 - 89.80: 8 Dihedral angle restraints: 3718 sinusoidal: 1557 harmonic: 2161 Sorted by residual: dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 237 " pdb=" CB CYS A 237 " ideal model delta sinusoidal sigma weight residual 93.00 -178.14 -88.86 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CB CYS D 61 " pdb=" SG CYS D 61 " pdb=" SG CYS D 66 " pdb=" CB CYS D 66 " ideal model delta sinusoidal sigma weight residual 93.00 6.87 86.13 1 1.00e+01 1.00e-02 8.95e+01 dihedral pdb=" CB CYS D 19 " pdb=" SG CYS D 19 " pdb=" SG CYS D 75 " pdb=" CB CYS D 75 " ideal model delta sinusoidal sigma weight residual 93.00 160.84 -67.84 1 1.00e+01 1.00e-02 5.98e+01 ... (remaining 3715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 574 0.059 - 0.118: 240 0.118 - 0.176: 74 0.176 - 0.235: 14 0.235 - 0.294: 3 Chirality restraints: 905 Sorted by residual: chirality pdb=" CB VAL A 515 " pdb=" CA VAL A 515 " pdb=" CG1 VAL A 515 " pdb=" CG2 VAL A 515 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA TYR D 16 " pdb=" N TYR D 16 " pdb=" C TYR D 16 " pdb=" CB TYR D 16 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ASN A 541 " pdb=" N ASN A 541 " pdb=" C ASN A 541 " pdb=" CB ASN A 541 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 902 not shown) Planarity restraints: 1070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 16 " -0.036 2.00e-02 2.50e+03 3.14e-02 1.98e+01 pdb=" CG TYR D 16 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TYR D 16 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR D 16 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR D 16 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 16 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR D 16 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 16 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 579 " 0.023 2.00e-02 2.50e+03 2.46e-02 1.21e+01 pdb=" CG TYR A 579 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR A 579 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 579 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR A 579 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR A 579 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 579 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 579 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 337 " -0.017 2.00e-02 2.50e+03 3.37e-02 1.13e+01 pdb=" CG ASN A 337 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN A 337 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 337 " -0.020 2.00e-02 2.50e+03 ... (remaining 1067 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 164 2.56 - 3.14: 5673 3.14 - 3.73: 9188 3.73 - 4.31: 12124 4.31 - 4.90: 18616 Nonbonded interactions: 45765 Sorted by model distance: nonbonded pdb=" O SER A 540 " pdb=" OD1 ASN A 541 " model vdw 1.974 3.040 nonbonded pdb=" OD1 ASN A 541 " pdb=" OD1 ASP A 542 " model vdw 2.004 3.040 nonbonded pdb=" NZ LYS C 557 " pdb=" OG1 THR C 560 " model vdw 2.051 3.120 nonbonded pdb=" O GLU A 443 " pdb=" OG SER A 446 " model vdw 2.104 3.040 nonbonded pdb=" O THR A 571 " pdb=" OG1 THR A 578 " model vdw 2.109 3.040 ... (remaining 45760 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.580 Find NCS groups from input model: 0.060 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 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 : 0.009 0.087 6172 Z= 0.623 Angle : 1.376 12.295 8363 Z= 0.789 Chirality : 0.071 0.294 905 Planarity : 0.008 0.061 1070 Dihedral : 17.387 89.796 2275 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 49.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.25 % Favored : 77.75 % Rotamer: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -5.01 (0.26), residues: 719 helix: -2.92 (0.42), residues: 92 sheet: -2.21 (0.53), residues: 80 loop : -3.94 (0.23), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP A 183 HIS 0.022 0.004 HIS A 264 PHE 0.038 0.005 PHE A 231 TYR 0.077 0.005 TYR D 16 ARG 0.021 0.002 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8079 (mmt180) cc_final: 0.7387 (mmt90) REVERT: A 221 ASP cc_start: 0.7618 (m-30) cc_final: 0.7305 (p0) REVERT: A 310 LYS cc_start: 0.7883 (ttpp) cc_final: 0.7662 (pttp) REVERT: A 454 ARG cc_start: 0.7256 (mtt-85) cc_final: 0.6858 (mtt-85) REVERT: A 504 MET cc_start: 0.3325 (mmm) cc_final: 0.2903 (mmm) REVERT: A 553 MET cc_start: 0.8012 (mmm) cc_final: 0.7723 (mmm) REVERT: C 567 LYS cc_start: 0.3880 (mttm) cc_final: 0.2171 (ptmt) REVERT: C 695 GLU cc_start: 0.8748 (pm20) cc_final: 0.8295 (pm20) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2146 time to fit residues: 42.3933 Evaluate side-chains 137 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 chunk 18 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN D 4 GLN D 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.165326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.147364 restraints weight = 16268.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.150995 restraints weight = 10029.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.154007 restraints weight = 6437.149| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6172 Z= 0.264 Angle : 0.936 10.211 8363 Z= 0.475 Chirality : 0.054 0.221 905 Planarity : 0.006 0.069 1070 Dihedral : 7.723 27.930 805 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.02 % Favored : 84.98 % Rotamer: Outliers : 2.80 % Allowed : 16.67 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -4.58 (0.27), residues: 719 helix: -2.61 (0.45), residues: 96 sheet: -2.55 (0.44), residues: 106 loop : -3.52 (0.24), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 551 HIS 0.013 0.002 HIS A 264 PHE 0.017 0.002 PHE A 506 TYR 0.043 0.002 TYR D 16 ARG 0.006 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.6281 (pmm) cc_final: 0.5793 (pmm) REVERT: A 102 LYS cc_start: 0.8601 (pttm) cc_final: 0.8393 (mmtp) REVERT: A 383 ARG cc_start: 0.8284 (mtt180) cc_final: 0.7842 (mtm110) REVERT: A 465 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7337 (mp10) REVERT: C 572 PHE cc_start: 0.8913 (m-80) cc_final: 0.8696 (m-80) REVERT: C 591 ASP cc_start: 0.5144 (t0) cc_final: 0.4680 (t0) REVERT: D 13 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8290 (mt-10) REVERT: D 76 ASN cc_start: 0.7878 (m-40) cc_final: 0.6931 (m-40) outliers start: 19 outliers final: 14 residues processed: 174 average time/residue: 0.2051 time to fit residues: 45.2502 Evaluate side-chains 168 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain D residue 27 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS C 711 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.160828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.142373 restraints weight = 16818.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.146381 restraints weight = 10695.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.149417 restraints weight = 6647.000| |-----------------------------------------------------------------------------| r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6172 Z= 0.348 Angle : 0.904 9.435 8363 Z= 0.467 Chirality : 0.054 0.235 905 Planarity : 0.007 0.059 1070 Dihedral : 7.664 42.481 805 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 25.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 16.55 % Favored : 83.31 % Rotamer: Outliers : 5.16 % Allowed : 22.12 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -4.58 (0.27), residues: 719 helix: -2.29 (0.47), residues: 95 sheet: -2.71 (0.45), residues: 104 loop : -3.55 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 133 HIS 0.009 0.002 HIS A 548 PHE 0.019 0.002 PHE A 381 TYR 0.034 0.002 TYR D 16 ARG 0.007 0.001 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8099 (tpp) cc_final: 0.7851 (tpt) REVERT: A 102 LYS cc_start: 0.8739 (pttm) cc_final: 0.8487 (pttm) REVERT: A 120 GLU cc_start: 0.8412 (tp30) cc_final: 0.7992 (tp30) REVERT: A 221 ASP cc_start: 0.7365 (m-30) cc_final: 0.7163 (p0) REVERT: A 369 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6672 (mtpt) REVERT: A 383 ARG cc_start: 0.8387 (mtt180) cc_final: 0.7962 (mtm110) REVERT: A 404 ASP cc_start: 0.8831 (t0) cc_final: 0.8534 (t0) REVERT: C 486 LEU cc_start: 0.8661 (tp) cc_final: 0.8439 (mp) REVERT: C 553 MET cc_start: 0.7012 (ttp) cc_final: 0.6794 (ttp) REVERT: C 559 TRP cc_start: 0.0379 (OUTLIER) cc_final: -0.3609 (m-10) REVERT: C 587 TYR cc_start: 0.6781 (OUTLIER) cc_final: 0.6133 (m-80) REVERT: D 13 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8385 (mt-10) outliers start: 35 outliers final: 25 residues processed: 169 average time/residue: 0.2067 time to fit residues: 44.5700 Evaluate side-chains 170 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 251 TRP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 559 TRP Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 579 TYR Chi-restraints excluded: chain C residue 587 TYR Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 27 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 0.2980 chunk 65 optimal weight: 0.9990 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 78 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.164157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.145700 restraints weight = 16628.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.150041 restraints weight = 10228.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.153058 restraints weight = 6117.892| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6172 Z= 0.217 Angle : 0.816 9.101 8363 Z= 0.407 Chirality : 0.051 0.226 905 Planarity : 0.006 0.074 1070 Dihedral : 6.924 32.105 805 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.63 % Favored : 86.37 % Rotamer: Outliers : 5.46 % Allowed : 26.70 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -4.09 (0.28), residues: 719 helix: -1.86 (0.51), residues: 93 sheet: -2.20 (0.51), residues: 91 loop : -3.24 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 551 HIS 0.008 0.001 HIS D 10 PHE 0.017 0.002 PHE A 428 TYR 0.024 0.002 TYR D 16 ARG 0.005 0.001 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.6530 (pmm) cc_final: 0.6178 (pmm) REVERT: A 83 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7243 (mtp180) REVERT: A 102 LYS cc_start: 0.8663 (pttm) cc_final: 0.8440 (mmtp) REVERT: A 313 HIS cc_start: 0.3078 (OUTLIER) cc_final: 0.1700 (m-70) REVERT: A 383 ARG cc_start: 0.8368 (mtt180) cc_final: 0.7958 (mtm110) REVERT: A 404 ASP cc_start: 0.8763 (t0) cc_final: 0.8563 (t0) REVERT: A 465 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7305 (mp10) REVERT: A 482 PHE cc_start: 0.1023 (OUTLIER) cc_final: 0.0020 (t80) REVERT: A 500 LEU cc_start: 0.8147 (pp) cc_final: 0.7735 (tt) REVERT: C 587 TYR cc_start: 0.6710 (OUTLIER) cc_final: 0.6035 (m-80) REVERT: C 591 ASP cc_start: 0.5621 (t0) cc_final: 0.5073 (t0) REVERT: D 76 ASN cc_start: 0.8635 (m-40) cc_final: 0.8049 (t0) outliers start: 37 outliers final: 25 residues processed: 169 average time/residue: 0.1941 time to fit residues: 42.1126 Evaluate side-chains 171 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 587 TYR Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 27 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 1 optimal weight: 0.1980 chunk 31 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.165613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.147082 restraints weight = 16399.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.151391 restraints weight = 10129.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.154395 restraints weight = 6121.283| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6172 Z= 0.218 Angle : 0.803 9.198 8363 Z= 0.402 Chirality : 0.050 0.216 905 Planarity : 0.005 0.059 1070 Dihedral : 6.567 30.299 805 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.21 % Favored : 86.79 % Rotamer: Outliers : 6.05 % Allowed : 26.70 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.75 (0.29), residues: 719 helix: -1.71 (0.53), residues: 93 sheet: -1.75 (0.56), residues: 86 loop : -3.02 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 412 HIS 0.004 0.001 HIS D 10 PHE 0.016 0.002 PHE D 25 TYR 0.023 0.002 TYR D 16 ARG 0.006 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7042 (mtp180) REVERT: A 102 LYS cc_start: 0.8597 (pttm) cc_final: 0.8385 (mmtp) REVERT: A 125 LEU cc_start: 0.8629 (mt) cc_final: 0.8391 (mt) REVERT: A 265 LYS cc_start: 0.7223 (tmtt) cc_final: 0.7014 (tppt) REVERT: A 313 HIS cc_start: 0.2999 (OUTLIER) cc_final: 0.1716 (m-70) REVERT: A 369 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6257 (tttt) REVERT: A 383 ARG cc_start: 0.8351 (mtt180) cc_final: 0.7978 (mtm110) REVERT: A 404 ASP cc_start: 0.8714 (t0) cc_final: 0.8479 (t0) REVERT: A 465 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7303 (mp10) REVERT: A 482 PHE cc_start: 0.0870 (OUTLIER) cc_final: 0.0267 (t80) REVERT: C 551 TRP cc_start: 0.7790 (t-100) cc_final: 0.7402 (t60) REVERT: C 559 TRP cc_start: 0.0171 (OUTLIER) cc_final: -0.3215 (m-10) REVERT: C 587 TYR cc_start: 0.6693 (OUTLIER) cc_final: 0.5992 (m-80) REVERT: C 591 ASP cc_start: 0.5225 (t0) cc_final: 0.4731 (t0) outliers start: 41 outliers final: 26 residues processed: 171 average time/residue: 0.1935 time to fit residues: 42.2519 Evaluate side-chains 171 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 251 TRP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 559 TRP Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 572 PHE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 579 TYR Chi-restraints excluded: chain C residue 587 TYR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 27 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 38 optimal weight: 0.0040 chunk 70 optimal weight: 6.9990 chunk 53 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 chunk 28 optimal weight: 0.0470 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.1094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 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 = 0.4370 r_free = 0.4370 target = 0.165300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.146624 restraints weight = 16185.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.151090 restraints weight = 10175.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.153842 restraints weight = 6066.776| |-----------------------------------------------------------------------------| r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6172 Z= 0.221 Angle : 0.805 11.573 8363 Z= 0.401 Chirality : 0.049 0.192 905 Planarity : 0.005 0.084 1070 Dihedral : 6.452 29.948 805 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.77 % Favored : 86.23 % Rotamer: Outliers : 5.90 % Allowed : 27.58 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -3.64 (0.29), residues: 719 helix: -1.80 (0.52), residues: 94 sheet: -1.86 (0.54), residues: 92 loop : -2.88 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 551 HIS 0.012 0.001 HIS D 10 PHE 0.014 0.002 PHE A 503 TYR 0.021 0.002 TYR D 16 ARG 0.007 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.6970 (mtp180) REVERT: A 125 LEU cc_start: 0.8668 (mt) cc_final: 0.8443 (mt) REVERT: A 313 HIS cc_start: 0.2944 (OUTLIER) cc_final: 0.1701 (m-70) REVERT: A 362 GLU cc_start: 0.6661 (mm-30) cc_final: 0.6460 (mm-30) REVERT: A 369 LYS cc_start: 0.6791 (OUTLIER) cc_final: 0.6228 (tttt) REVERT: A 383 ARG cc_start: 0.8393 (mtt180) cc_final: 0.7995 (mtm110) REVERT: A 404 ASP cc_start: 0.8724 (t0) cc_final: 0.8492 (t0) REVERT: A 465 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7166 (mp10) REVERT: A 500 LEU cc_start: 0.7825 (pp) cc_final: 0.7552 (tt) REVERT: A 553 MET cc_start: 0.8059 (mmm) cc_final: 0.7661 (mmm) REVERT: C 559 TRP cc_start: 0.0217 (OUTLIER) cc_final: -0.3204 (m-10) REVERT: C 587 TYR cc_start: 0.6675 (OUTLIER) cc_final: 0.5713 (m-80) REVERT: C 591 ASP cc_start: 0.5158 (t0) cc_final: 0.4685 (t0) outliers start: 40 outliers final: 31 residues processed: 167 average time/residue: 0.2045 time to fit residues: 43.6626 Evaluate side-chains 174 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 251 TRP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 559 TRP Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 572 PHE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 579 TYR Chi-restraints excluded: chain C residue 587 TYR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 27 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 70 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 0.0770 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 189 GLN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.163646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.145012 restraints weight = 16228.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.149170 restraints weight = 10377.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.152343 restraints weight = 6328.296| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6172 Z= 0.246 Angle : 0.818 9.772 8363 Z= 0.408 Chirality : 0.050 0.196 905 Planarity : 0.005 0.074 1070 Dihedral : 6.457 33.115 805 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.19 % Favored : 85.81 % Rotamer: Outliers : 6.19 % Allowed : 28.47 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.63 (0.29), residues: 719 helix: -1.88 (0.52), residues: 94 sheet: -1.69 (0.55), residues: 87 loop : -2.88 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 133 HIS 0.014 0.002 HIS D 10 PHE 0.020 0.002 PHE A 258 TYR 0.024 0.002 TYR D 16 ARG 0.007 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8187 (mm-30) REVERT: A 83 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7057 (mtp180) REVERT: A 102 LYS cc_start: 0.8695 (pttm) cc_final: 0.8343 (mmtp) REVERT: A 313 HIS cc_start: 0.3060 (OUTLIER) cc_final: 0.2715 (t-90) REVERT: A 362 GLU cc_start: 0.6308 (mm-30) cc_final: 0.6026 (mm-30) REVERT: A 369 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6337 (tttt) REVERT: A 383 ARG cc_start: 0.8343 (mtt180) cc_final: 0.7923 (mtm110) REVERT: A 386 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7679 (mtt180) REVERT: A 464 ASP cc_start: 0.8246 (p0) cc_final: 0.7792 (p0) REVERT: A 500 LEU cc_start: 0.8001 (pp) cc_final: 0.7683 (tt) REVERT: A 551 TRP cc_start: 0.6238 (t-100) cc_final: 0.5931 (t-100) REVERT: C 559 TRP cc_start: 0.0566 (OUTLIER) cc_final: -0.3007 (m-10) REVERT: C 567 LYS cc_start: 0.3445 (ttmt) cc_final: 0.3150 (tttt) REVERT: C 587 TYR cc_start: 0.6592 (OUTLIER) cc_final: 0.5947 (m-80) REVERT: C 591 ASP cc_start: 0.5556 (t0) cc_final: 0.5054 (t0) outliers start: 42 outliers final: 32 residues processed: 172 average time/residue: 0.2020 time to fit residues: 44.0039 Evaluate side-chains 175 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 251 TRP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 559 TRP Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 572 PHE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 579 TYR Chi-restraints excluded: chain C residue 587 TYR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 76 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 50 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.163133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.144480 restraints weight = 15955.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.148863 restraints weight = 10191.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.152103 restraints weight = 6122.549| |-----------------------------------------------------------------------------| r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6172 Z= 0.266 Angle : 0.864 13.055 8363 Z= 0.428 Chirality : 0.051 0.208 905 Planarity : 0.006 0.083 1070 Dihedral : 6.501 32.644 805 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.05 % Favored : 85.95 % Rotamer: Outliers : 6.19 % Allowed : 28.02 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.55 (0.29), residues: 719 helix: -1.85 (0.52), residues: 94 sheet: -1.29 (0.57), residues: 79 loop : -2.87 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 551 HIS 0.012 0.001 HIS D 10 PHE 0.016 0.002 PHE A 258 TYR 0.027 0.002 TYR D 16 ARG 0.008 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7073 (mtp180) REVERT: A 102 LYS cc_start: 0.8659 (pttm) cc_final: 0.8324 (mmtp) REVERT: A 313 HIS cc_start: 0.3069 (OUTLIER) cc_final: 0.2711 (t-90) REVERT: A 362 GLU cc_start: 0.6168 (mm-30) cc_final: 0.5940 (mm-30) REVERT: A 369 LYS cc_start: 0.6809 (OUTLIER) cc_final: 0.6246 (tttt) REVERT: A 383 ARG cc_start: 0.8386 (mtt180) cc_final: 0.7920 (mtm110) REVERT: A 386 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7586 (mtt180) REVERT: A 404 ASP cc_start: 0.8797 (t0) cc_final: 0.8572 (t0) REVERT: A 465 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7210 (mp10) REVERT: A 500 LEU cc_start: 0.7998 (pp) cc_final: 0.7660 (tt) REVERT: C 488 ARG cc_start: 0.8091 (tpt170) cc_final: 0.7658 (ttt90) REVERT: C 559 TRP cc_start: 0.0185 (OUTLIER) cc_final: -0.3222 (m-10) REVERT: C 587 TYR cc_start: 0.6591 (OUTLIER) cc_final: 0.5929 (m-80) REVERT: C 591 ASP cc_start: 0.5727 (t0) cc_final: 0.5176 (t0) REVERT: D 74 TYR cc_start: 0.7128 (m-80) cc_final: 0.6901 (m-80) outliers start: 42 outliers final: 34 residues processed: 167 average time/residue: 0.1982 time to fit residues: 41.9347 Evaluate side-chains 181 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 251 TRP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 489 TRP Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 548 HIS Chi-restraints excluded: chain C residue 559 TRP Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 572 PHE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 579 TYR Chi-restraints excluded: chain C residue 587 TYR Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 76 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 44 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.165136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.146184 restraints weight = 15792.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.150717 restraints weight = 10029.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.154033 restraints weight = 5974.946| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6172 Z= 0.231 Angle : 0.864 12.270 8363 Z= 0.422 Chirality : 0.050 0.215 905 Planarity : 0.005 0.075 1070 Dihedral : 6.350 29.767 805 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.07 % Favored : 86.93 % Rotamer: Outliers : 6.05 % Allowed : 28.32 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -3.36 (0.30), residues: 719 helix: -1.93 (0.51), residues: 94 sheet: -1.24 (0.60), residues: 78 loop : -2.67 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 551 HIS 0.016 0.002 HIS C 548 PHE 0.019 0.002 PHE A 258 TYR 0.029 0.002 TYR A 277 ARG 0.009 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 6 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8197 (mm-30) REVERT: A 83 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.6873 (mtt-85) REVERT: A 102 LYS cc_start: 0.8654 (pttm) cc_final: 0.8249 (mmtp) REVERT: A 125 LEU cc_start: 0.8262 (mt) cc_final: 0.8051 (mt) REVERT: A 313 HIS cc_start: 0.3351 (OUTLIER) cc_final: 0.2891 (t-90) REVERT: A 362 GLU cc_start: 0.6202 (mm-30) cc_final: 0.5944 (mm-30) REVERT: A 369 LYS cc_start: 0.6682 (OUTLIER) cc_final: 0.6121 (tttt) REVERT: A 383 ARG cc_start: 0.8372 (mtt180) cc_final: 0.7914 (mtm110) REVERT: A 386 ARG cc_start: 0.7961 (mtt180) cc_final: 0.7614 (mtt180) REVERT: A 464 ASP cc_start: 0.8234 (p0) cc_final: 0.7623 (p0) REVERT: A 465 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7040 (mp10) REVERT: A 482 PHE cc_start: 0.1356 (OUTLIER) cc_final: 0.0499 (t80) REVERT: A 500 LEU cc_start: 0.8034 (pp) cc_final: 0.7706 (tt) REVERT: C 559 TRP cc_start: 0.0497 (OUTLIER) cc_final: -0.3085 (m-10) REVERT: C 587 TYR cc_start: 0.6701 (OUTLIER) cc_final: 0.5710 (m-80) REVERT: C 591 ASP cc_start: 0.5337 (t0) cc_final: 0.4862 (t0) REVERT: D 74 TYR cc_start: 0.6975 (m-80) cc_final: 0.6758 (m-80) outliers start: 41 outliers final: 31 residues processed: 173 average time/residue: 0.2052 time to fit residues: 44.7603 Evaluate side-chains 176 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 251 TRP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 489 TRP Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 559 TRP Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 572 PHE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 579 TYR Chi-restraints excluded: chain C residue 587 TYR Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 76 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 48 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 61 optimal weight: 0.0970 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 47 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.166739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.147702 restraints weight = 16009.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.152183 restraints weight = 10022.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.155419 restraints weight = 5958.365| |-----------------------------------------------------------------------------| r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6172 Z= 0.216 Angle : 0.878 18.412 8363 Z= 0.424 Chirality : 0.050 0.227 905 Planarity : 0.006 0.077 1070 Dihedral : 6.216 26.258 805 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.52 % Favored : 87.48 % Rotamer: Outliers : 5.75 % Allowed : 29.20 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -3.18 (0.30), residues: 719 helix: -1.84 (0.52), residues: 90 sheet: -1.23 (0.60), residues: 80 loop : -2.51 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 551 HIS 0.011 0.002 HIS A 417 PHE 0.021 0.002 PHE A 39 TYR 0.019 0.001 TYR A 512 ARG 0.010 0.001 ARG A 409 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8203 (mm-30) REVERT: A 98 MET cc_start: 0.6183 (tpp) cc_final: 0.5855 (tpp) REVERT: A 102 LYS cc_start: 0.8443 (pttm) cc_final: 0.8030 (mmtt) REVERT: A 313 HIS cc_start: 0.3141 (OUTLIER) cc_final: 0.2607 (t-90) REVERT: A 362 GLU cc_start: 0.6622 (mm-30) cc_final: 0.6418 (mm-30) REVERT: A 369 LYS cc_start: 0.6640 (OUTLIER) cc_final: 0.6085 (tttt) REVERT: A 383 ARG cc_start: 0.8354 (mtt180) cc_final: 0.7908 (mtm110) REVERT: A 386 ARG cc_start: 0.7946 (mtt180) cc_final: 0.7693 (mtt180) REVERT: A 404 ASP cc_start: 0.8558 (t0) cc_final: 0.8335 (t0) REVERT: A 409 ARG cc_start: 0.7042 (ttp80) cc_final: 0.6469 (ptp-110) REVERT: A 465 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7146 (mp10) REVERT: A 482 PHE cc_start: 0.0724 (OUTLIER) cc_final: 0.0283 (t80) REVERT: A 500 LEU cc_start: 0.8032 (pp) cc_final: 0.7712 (tt) REVERT: C 559 TRP cc_start: 0.0477 (OUTLIER) cc_final: -0.3197 (m-10) REVERT: C 572 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8629 (t80) REVERT: C 587 TYR cc_start: 0.6634 (OUTLIER) cc_final: 0.5672 (m-80) REVERT: C 591 ASP cc_start: 0.5074 (t0) cc_final: 0.4798 (t0) outliers start: 39 outliers final: 27 residues processed: 174 average time/residue: 0.1991 time to fit residues: 44.2696 Evaluate side-chains 177 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 251 TRP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 489 TRP Chi-restraints excluded: chain C residue 559 TRP Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 572 PHE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 579 TYR Chi-restraints excluded: chain C residue 587 TYR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 76 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 chunk 41 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.167322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.148214 restraints weight = 16167.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.152745 restraints weight = 10098.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.156032 restraints weight = 6033.248| |-----------------------------------------------------------------------------| r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6172 Z= 0.219 Angle : 0.850 13.333 8363 Z= 0.415 Chirality : 0.050 0.225 905 Planarity : 0.006 0.075 1070 Dihedral : 6.096 26.322 805 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % Rotamer: Outliers : 5.60 % Allowed : 29.50 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -3.13 (0.30), residues: 719 helix: -1.83 (0.53), residues: 90 sheet: -1.16 (0.60), residues: 80 loop : -2.48 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 551 HIS 0.010 0.001 HIS D 10 PHE 0.024 0.002 PHE A 39 TYR 0.036 0.002 TYR A 277 ARG 0.009 0.001 ARG A 409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2159.54 seconds wall clock time: 38 minutes 16.16 seconds (2296.16 seconds total)