Starting phenix.real_space_refine on Thu Jul 24 11:07:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bw8_30230/07_2025/7bw8_30230.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bw8_30230/07_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_30230/07_2025/7bw8_30230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bw8_30230/07_2025/7bw8_30230.map" model { file = "/net/cci-nas-00/data/ceres_data/7bw8_30230/07_2025/7bw8_30230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bw8_30230/07_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-5711/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: 3.74, per 1000 atoms: 0.62 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: 1.38 Conformation dependent library (CDL) restraints added in 830.2 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: 0.59 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: 1.41 Time building geometry restraints manager: 1.69 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: 0.290 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.820 Find NCS groups from input model: 0.050 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.310 ------------------------------------------------------------------------------- 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 : 0.010 0.322 6187 Z= 0.511 Angle : 1.402 15.154 8393 Z= 0.798 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 Details of bonding type rmsd hydrogen bonds : bond 0.23539 ( 101) hydrogen bonds : angle 10.90443 ( 258) SS BOND : bond 0.08392 ( 15) SS BOND : angle 4.62743 ( 30) covalent geometry : bond 0.00943 ( 6172) covalent geometry : angle 1.37647 ( 8363) *********************** 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 : 0.630 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: 0.2094 time to fit residues: 41.3571 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 : 0.656 ------------------------------------------------------------------------------- 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: 0.2980 chunk 18 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.165244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.146498 restraints weight = 16255.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.149867 restraints weight = 9905.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.152179 restraints weight = 6874.078| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6187 Z= 0.184 Angle : 0.952 10.445 8393 Z= 0.482 Chirality : 0.054 0.225 905 Planarity : 0.006 0.072 1070 Dihedral : 7.777 27.442 805 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 23.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.30 % Favored : 84.70 % Rotamer: Outliers : 2.95 % Allowed : 15.78 % Favored : 81.27 % 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: -4.63 (0.27), residues: 719 helix: -2.63 (0.44), residues: 96 sheet: -2.59 (0.45), residues: 102 loop : -3.55 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 551 HIS 0.013 0.002 HIS A 264 PHE 0.016 0.002 PHE A 506 TYR 0.045 0.002 TYR D 16 ARG 0.004 0.001 ARG C 702 Details of bonding type rmsd hydrogen bonds : bond 0.06071 ( 101) hydrogen bonds : angle 8.61851 ( 258) SS BOND : bond 0.00833 ( 15) SS BOND : angle 2.06288 ( 30) covalent geometry : bond 0.00405 ( 6172) covalent geometry : angle 0.94607 ( 8363) *********************** 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 184 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.6503 (pmm) cc_final: 0.5984 (pmm) REVERT: A 383 ARG cc_start: 0.8312 (mtt180) cc_final: 0.7841 (mtm110) REVERT: A 465 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7430 (mp10) REVERT: A 553 MET cc_start: 0.7606 (mmm) cc_final: 0.7149 (mmm) REVERT: C 591 ASP cc_start: 0.5351 (t0) cc_final: 0.4824 (t0) REVERT: D 13 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8292 (mt-10) REVERT: D 74 TYR cc_start: 0.7364 (OUTLIER) cc_final: 0.7070 (t80) REVERT: D 76 ASN cc_start: 0.8018 (m110) cc_final: 0.7548 (m110) outliers start: 20 outliers final: 14 residues processed: 172 average time/residue: 0.1991 time to fit residues: 43.4749 Evaluate side-chains 170 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 74 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 49 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN C 711 ASN D 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.163293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.144823 restraints weight = 16480.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.148987 restraints weight = 10139.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.151664 restraints weight = 6209.004| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6187 Z= 0.179 Angle : 0.847 8.731 8393 Z= 0.433 Chirality : 0.052 0.229 905 Planarity : 0.006 0.063 1070 Dihedral : 7.305 32.170 805 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.30 % Favored : 84.70 % Rotamer: Outliers : 4.57 % Allowed : 21.24 % Favored : 74.19 % 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: -4.40 (0.27), residues: 719 helix: -2.33 (0.47), residues: 96 sheet: -2.47 (0.47), residues: 98 loop : -3.40 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 412 HIS 0.009 0.002 HIS A 264 PHE 0.015 0.002 PHE D 24 TYR 0.034 0.002 TYR D 16 ARG 0.008 0.001 ARG A 409 Details of bonding type rmsd hydrogen bonds : bond 0.04945 ( 101) hydrogen bonds : angle 8.19910 ( 258) SS BOND : bond 0.00765 ( 15) SS BOND : angle 1.83670 ( 30) covalent geometry : bond 0.00397 ( 6172) covalent geometry : angle 0.84138 ( 8363) *********************** 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 180 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8383 (mmtp) cc_final: 0.8170 (mmtp) REVERT: A 383 ARG cc_start: 0.8283 (mtt180) cc_final: 0.7848 (mtm110) REVERT: A 465 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: A 553 MET cc_start: 0.7888 (mmm) cc_final: 0.7653 (mmm) REVERT: C 591 ASP cc_start: 0.4717 (t0) cc_final: 0.4278 (t0) REVERT: D 13 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8336 (mt-10) REVERT: D 76 ASN cc_start: 0.8341 (m-40) cc_final: 0.8082 (m110) outliers start: 31 outliers final: 22 residues processed: 162 average time/residue: 0.2626 time to fit residues: 54.6939 Evaluate side-chains 167 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 274 CYS Chi-restraints excluded: chain A residue 341 ILE 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 482 PHE Chi-restraints excluded: chain A residue 485 ILE 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 566 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain C residue 572 PHE Chi-restraints excluded: chain C residue 578 THR 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: 1.9990 chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 44 optimal weight: 0.0870 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 0.0770 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 overall best weight: 1.2120 ------------------------------------------------------------------------------- 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 546 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.165120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.146434 restraints weight = 16666.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.150836 restraints weight = 10414.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.153743 restraints weight = 6268.746| |-----------------------------------------------------------------------------| r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6187 Z= 0.154 Angle : 0.790 9.131 8393 Z= 0.402 Chirality : 0.050 0.227 905 Planarity : 0.005 0.051 1070 Dihedral : 6.847 31.083 805 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.77 % Favored : 86.23 % Rotamer: Outliers : 5.16 % Allowed : 24.48 % Favored : 70.35 % 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: -3.97 (0.28), residues: 719 helix: -1.89 (0.51), residues: 93 sheet: -1.94 (0.54), residues: 85 loop : -3.17 (0.24), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 412 HIS 0.008 0.001 HIS D 10 PHE 0.018 0.002 PHE A 428 TYR 0.026 0.002 TYR D 16 ARG 0.006 0.001 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 101) hydrogen bonds : angle 7.74309 ( 258) SS BOND : bond 0.00580 ( 15) SS BOND : angle 1.72201 ( 30) covalent geometry : bond 0.00340 ( 6172) covalent geometry : angle 0.78508 ( 8363) *********************** 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 187 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 1.396 Fit side-chains revert: symmetry clash REVERT: A 11 MET cc_start: 0.6777 (pmm) cc_final: 0.6512 (pmm) REVERT: A 83 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7054 (mtp180) REVERT: A 102 LYS cc_start: 0.8437 (mmtp) cc_final: 0.8156 (mmtp) REVERT: A 313 HIS cc_start: 0.2969 (OUTLIER) cc_final: 0.1616 (m-70) REVERT: A 383 ARG cc_start: 0.8336 (mtt180) cc_final: 0.7944 (mtm110) REVERT: A 465 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7429 (mp10) REVERT: A 482 PHE cc_start: 0.1244 (OUTLIER) cc_final: 0.0339 (t80) REVERT: A 500 LEU cc_start: 0.8162 (pp) cc_final: 0.7772 (tt) REVERT: A 553 MET cc_start: 0.7927 (mmm) cc_final: 0.7516 (mmm) REVERT: C 587 TYR cc_start: 0.6653 (OUTLIER) cc_final: 0.5984 (m-80) REVERT: C 591 ASP cc_start: 0.5260 (t0) cc_final: 0.4686 (t0) outliers start: 35 outliers final: 25 residues processed: 169 average time/residue: 0.2807 time to fit residues: 62.7838 Evaluate side-chains 174 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 117 VAL 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 405 ASN Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 465 GLN 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 570 VAL 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 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: 2.9990 chunk 3 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** 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 = 0.4278 r_free = 0.4278 target = 0.158194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.139910 restraints weight = 16825.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.143708 restraints weight = 10897.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.146058 restraints weight = 6858.654| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 6187 Z= 0.291 Angle : 0.942 8.775 8393 Z= 0.494 Chirality : 0.056 0.244 905 Planarity : 0.006 0.060 1070 Dihedral : 7.588 44.400 805 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 27.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.80 % Favored : 82.20 % Rotamer: Outliers : 6.93 % Allowed : 26.11 % Favored : 66.96 % 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: -4.07 (0.28), residues: 719 helix: -1.81 (0.51), residues: 90 sheet: -2.19 (0.52), residues: 88 loop : -3.23 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 183 HIS 0.009 0.002 HIS D 10 PHE 0.025 0.003 PHE A 381 TYR 0.027 0.003 TYR D 16 ARG 0.009 0.001 ARG A 577 Details of bonding type rmsd hydrogen bonds : bond 0.05127 ( 101) hydrogen bonds : angle 8.01680 ( 258) SS BOND : bond 0.00576 ( 15) SS BOND : angle 1.97533 ( 30) covalent geometry : bond 0.00660 ( 6172) covalent geometry : angle 0.93630 ( 8363) *********************** 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 195 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7216 (mtp180) REVERT: A 189 GLN cc_start: 0.6754 (OUTLIER) cc_final: 0.6497 (mt0) REVERT: A 221 ASP cc_start: 0.7526 (m-30) cc_final: 0.7321 (p0) REVERT: A 313 HIS cc_start: 0.2758 (OUTLIER) cc_final: 0.1321 (m-70) REVERT: A 362 GLU cc_start: 0.6414 (mm-30) cc_final: 0.6176 (mm-30) REVERT: A 383 ARG cc_start: 0.8402 (mtt180) cc_final: 0.8014 (mtm110) REVERT: A 404 ASP cc_start: 0.8863 (t0) cc_final: 0.8607 (t0) REVERT: A 464 ASP cc_start: 0.8486 (p0) cc_final: 0.8047 (p0) REVERT: C 488 ARG cc_start: 0.8357 (tpt170) cc_final: 0.7800 (ttt90) REVERT: C 559 TRP cc_start: 0.0152 (OUTLIER) cc_final: -0.3258 (m-10) REVERT: C 587 TYR cc_start: 0.6766 (OUTLIER) cc_final: 0.6195 (m-80) REVERT: D 76 ASN cc_start: 0.8389 (m110) cc_final: 0.8036 (m110) outliers start: 47 outliers final: 33 residues processed: 175 average time/residue: 0.3144 time to fit residues: 72.1883 Evaluate side-chains 182 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 54 LEU 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 189 GLN 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 343 ASN Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 437 SER 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 485 ILE 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 548 HIS Chi-restraints excluded: chain C residue 559 TRP Chi-restraints excluded: chain C residue 570 VAL 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 C residue 704 THR 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: 0.9990 chunk 70 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 28 optimal weight: 0.0370 chunk 47 optimal weight: 0.4980 chunk 58 optimal weight: 4.9990 chunk 50 optimal weight: 0.0570 chunk 71 optimal weight: 5.9990 chunk 61 optimal weight: 0.3980 chunk 9 optimal weight: 8.9990 overall best weight: 0.2976 ------------------------------------------------------------------------------- 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 548 HIS ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 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 = 0.4378 r_free = 0.4378 target = 0.166078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.147354 restraints weight = 15901.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.151898 restraints weight = 10043.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.155040 restraints weight = 5902.553| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6187 Z= 0.149 Angle : 0.858 12.242 8393 Z= 0.424 Chirality : 0.051 0.198 905 Planarity : 0.005 0.044 1070 Dihedral : 6.687 28.585 805 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 4.87 % Allowed : 29.79 % Favored : 65.34 % 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: -3.72 (0.29), residues: 719 helix: -1.90 (0.51), residues: 94 sheet: -1.71 (0.59), residues: 85 loop : -2.96 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 551 HIS 0.012 0.001 HIS D 10 PHE 0.019 0.002 PHE A 428 TYR 0.023 0.002 TYR D 16 ARG 0.009 0.001 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.04587 ( 101) hydrogen bonds : angle 7.36473 ( 258) SS BOND : bond 0.00425 ( 15) SS BOND : angle 1.64948 ( 30) covalent geometry : bond 0.00326 ( 6172) covalent geometry : angle 0.85429 ( 8363) *********************** 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 183 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 83 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7046 (mtp180) REVERT: A 102 LYS cc_start: 0.8377 (mmtp) cc_final: 0.8120 (mmtt) REVERT: A 313 HIS cc_start: 0.2902 (OUTLIER) cc_final: 0.1275 (m-70) REVERT: A 362 GLU cc_start: 0.6702 (mm-30) cc_final: 0.6501 (mm-30) REVERT: A 383 ARG cc_start: 0.8349 (mtt180) cc_final: 0.7857 (mtm110) REVERT: A 386 ARG cc_start: 0.7803 (mtt180) cc_final: 0.7467 (mtt180) REVERT: A 465 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7366 (mp10) REVERT: A 482 PHE cc_start: 0.0928 (OUTLIER) cc_final: 0.0127 (t80) REVERT: A 500 LEU cc_start: 0.8011 (pp) cc_final: 0.7682 (tt) REVERT: A 553 MET cc_start: 0.7857 (mmt) cc_final: 0.7632 (mmt) REVERT: C 559 TRP cc_start: 0.0508 (OUTLIER) cc_final: -0.3156 (m-10) REVERT: C 587 TYR cc_start: 0.6610 (OUTLIER) cc_final: 0.5911 (m-80) REVERT: C 591 ASP cc_start: 0.5764 (t0) cc_final: 0.5381 (t0) outliers start: 33 outliers final: 22 residues processed: 172 average time/residue: 0.2731 time to fit residues: 61.1458 Evaluate side-chains 167 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 201 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 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 568 THR Chi-restraints excluded: chain C residue 559 TRP 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 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: 4.9990 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 62 optimal weight: 0.0170 chunk 69 optimal weight: 2.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.166382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.147410 restraints weight = 15932.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.151897 restraints weight = 10093.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.155236 restraints weight = 6023.660| |-----------------------------------------------------------------------------| r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6187 Z= 0.143 Angle : 0.843 10.857 8393 Z= 0.420 Chirality : 0.050 0.207 905 Planarity : 0.005 0.063 1070 Dihedral : 6.404 27.433 805 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % Rotamer: Outliers : 5.31 % Allowed : 29.94 % Favored : 64.75 % 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: -3.47 (0.30), residues: 719 helix: -1.85 (0.52), residues: 90 sheet: -1.54 (0.56), residues: 87 loop : -2.75 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 551 HIS 0.012 0.001 HIS D 10 PHE 0.020 0.002 PHE A 39 TYR 0.018 0.002 TYR D 16 ARG 0.008 0.001 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 101) hydrogen bonds : angle 7.65843 ( 258) SS BOND : bond 0.00423 ( 15) SS BOND : angle 1.60839 ( 30) covalent geometry : bond 0.00324 ( 6172) covalent geometry : angle 0.83912 ( 8363) *********************** 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 181 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6932 (mtt-85) REVERT: A 86 ARG cc_start: 0.7729 (mtm110) cc_final: 0.7487 (mtp180) REVERT: A 313 HIS cc_start: 0.3080 (OUTLIER) cc_final: 0.1389 (m-70) REVERT: A 362 GLU cc_start: 0.6129 (mm-30) cc_final: 0.5874 (mm-30) REVERT: A 383 ARG cc_start: 0.8345 (mtt180) cc_final: 0.7901 (mtm110) REVERT: A 386 ARG cc_start: 0.7805 (mtt180) cc_final: 0.7437 (mtt180) REVERT: A 465 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7340 (mp10) REVERT: A 482 PHE cc_start: 0.0497 (OUTLIER) cc_final: 0.0038 (t80) REVERT: C 551 TRP cc_start: 0.7640 (t-100) cc_final: 0.7245 (t-100) REVERT: C 559 TRP cc_start: 0.0551 (OUTLIER) cc_final: -0.3133 (m-10) REVERT: C 587 TYR cc_start: 0.6598 (OUTLIER) cc_final: 0.5609 (m-80) REVERT: C 591 ASP cc_start: 0.5205 (t0) cc_final: 0.4774 (t0) outliers start: 36 outliers final: 28 residues processed: 166 average time/residue: 0.1965 time to fit residues: 42.6096 Evaluate side-chains 172 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU 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 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 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 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 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: 0.8980 chunk 48 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 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 = 0.4385 r_free = 0.4385 target = 0.166265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.147273 restraints weight = 15899.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.151940 restraints weight = 10120.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.155097 restraints weight = 5938.673| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6187 Z= 0.142 Angle : 0.841 9.528 8393 Z= 0.416 Chirality : 0.050 0.207 905 Planarity : 0.005 0.055 1070 Dihedral : 6.321 27.297 805 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.93 % Favored : 87.07 % Rotamer: Outliers : 6.64 % Allowed : 27.88 % Favored : 65.49 % 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: -3.34 (0.30), residues: 719 helix: -1.82 (0.53), residues: 90 sheet: -1.31 (0.61), residues: 79 loop : -2.66 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 551 HIS 0.011 0.001 HIS D 10 PHE 0.016 0.002 PHE A 39 TYR 0.021 0.002 TYR D 16 ARG 0.009 0.001 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.04058 ( 101) hydrogen bonds : angle 7.49207 ( 258) SS BOND : bond 0.00424 ( 15) SS BOND : angle 1.62262 ( 30) covalent geometry : bond 0.00323 ( 6172) covalent geometry : angle 0.83699 ( 8363) *********************** 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 192 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 147 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6946 (mtt-85) REVERT: A 86 ARG cc_start: 0.7696 (mtm110) cc_final: 0.7441 (mtp180) REVERT: A 102 LYS cc_start: 0.8312 (mmtt) cc_final: 0.8032 (mmtt) REVERT: A 265 LYS cc_start: 0.8303 (tppt) cc_final: 0.7625 (tmtt) REVERT: A 313 HIS cc_start: 0.2952 (OUTLIER) cc_final: 0.2525 (t-90) REVERT: A 383 ARG cc_start: 0.8337 (mtt180) cc_final: 0.7918 (mtm110) REVERT: A 386 ARG cc_start: 0.7921 (mtt180) cc_final: 0.7713 (mtt90) REVERT: A 465 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7417 (mp10) REVERT: A 500 LEU cc_start: 0.8053 (pp) cc_final: 0.7824 (tt) REVERT: A 514 ASN cc_start: 0.7942 (t0) cc_final: 0.7568 (t0) REVERT: C 504 MET cc_start: 0.6966 (mpp) cc_final: 0.6638 (mpp) REVERT: C 551 TRP cc_start: 0.7641 (t-100) cc_final: 0.7281 (t-100) REVERT: C 559 TRP cc_start: 0.0576 (OUTLIER) cc_final: -0.3160 (m-10) REVERT: C 587 TYR cc_start: 0.6600 (OUTLIER) cc_final: 0.5608 (m-80) REVERT: C 591 ASP cc_start: 0.5146 (t0) cc_final: 0.4718 (t0) outliers start: 45 outliers final: 33 residues processed: 177 average time/residue: 0.2252 time to fit residues: 52.2759 Evaluate side-chains 178 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 56 MET 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 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 532 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 569 LEU 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 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: 30.0000 chunk 40 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 0.0170 chunk 54 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS ** 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 = 0.4388 r_free = 0.4388 target = 0.166502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.147300 restraints weight = 16032.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.151800 restraints weight = 10233.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.155366 restraints weight = 6144.505| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6187 Z= 0.145 Angle : 0.848 10.409 8393 Z= 0.417 Chirality : 0.050 0.225 905 Planarity : 0.005 0.054 1070 Dihedral : 6.242 28.241 805 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.63 % Favored : 86.37 % Rotamer: Outliers : 6.19 % Allowed : 28.91 % 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: -3.36 (0.29), residues: 719 helix: -2.00 (0.51), residues: 94 sheet: -1.29 (0.61), residues: 79 loop : -2.64 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 551 HIS 0.010 0.001 HIS D 10 PHE 0.019 0.002 PHE A 39 TYR 0.028 0.002 TYR A 277 ARG 0.009 0.001 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 101) hydrogen bonds : angle 7.56951 ( 258) SS BOND : bond 0.00441 ( 15) SS BOND : angle 1.57473 ( 30) covalent geometry : bond 0.00330 ( 6172) covalent geometry : angle 0.84468 ( 8363) *********************** 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 189 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7034 (mtp180) REVERT: A 86 ARG cc_start: 0.7701 (mtm110) cc_final: 0.7446 (mtp180) REVERT: A 102 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7982 (mmtt) REVERT: A 265 LYS cc_start: 0.8256 (tppt) cc_final: 0.7658 (tmtt) REVERT: A 313 HIS cc_start: 0.3041 (OUTLIER) cc_final: 0.2516 (t-90) REVERT: A 362 GLU cc_start: 0.6646 (mm-30) cc_final: 0.6044 (mm-30) REVERT: A 383 ARG cc_start: 0.8439 (mtt180) cc_final: 0.8008 (mtm110) REVERT: A 386 ARG cc_start: 0.7935 (mtt180) cc_final: 0.7474 (mtt180) REVERT: A 409 ARG cc_start: 0.7024 (ttp80) cc_final: 0.6761 (ptp-110) REVERT: A 465 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7396 (mp10) REVERT: A 500 LEU cc_start: 0.8065 (pp) cc_final: 0.7787 (tt) REVERT: A 514 ASN cc_start: 0.7966 (t0) cc_final: 0.7594 (t0) REVERT: C 504 MET cc_start: 0.7070 (mpp) cc_final: 0.6788 (mpp) REVERT: C 551 TRP cc_start: 0.7703 (t-100) cc_final: 0.7292 (t-100) REVERT: C 559 TRP cc_start: 0.0429 (OUTLIER) cc_final: -0.3222 (m-10) REVERT: C 569 LEU cc_start: 0.8988 (mt) cc_final: 0.8728 (mp) REVERT: C 587 TYR cc_start: 0.6638 (OUTLIER) cc_final: 0.5656 (m-80) REVERT: C 591 ASP cc_start: 0.5174 (t0) cc_final: 0.4879 (t0) outliers start: 42 outliers final: 31 residues processed: 172 average time/residue: 0.2000 time to fit residues: 44.0769 Evaluate side-chains 174 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 56 MET 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 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 532 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 560 THR 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 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 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 48 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 7 optimal weight: 0.0770 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4405 r_free = 0.4405 target = 0.168059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.148891 restraints weight = 16012.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.153449 restraints weight = 10161.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.157021 restraints weight = 5994.707| |-----------------------------------------------------------------------------| r_work (final): 0.4279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6187 Z= 0.142 Angle : 0.878 13.705 8393 Z= 0.423 Chirality : 0.051 0.268 905 Planarity : 0.005 0.049 1070 Dihedral : 6.125 25.132 805 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.93 % Favored : 87.07 % Rotamer: Outliers : 5.31 % Allowed : 30.38 % Favored : 64.31 % 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: -3.17 (0.30), residues: 719 helix: -1.88 (0.53), residues: 90 sheet: -1.19 (0.62), residues: 79 loop : -2.50 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 551 HIS 0.009 0.001 HIS D 10 PHE 0.024 0.002 PHE A 39 TYR 0.020 0.001 TYR A 512 ARG 0.009 0.001 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 101) hydrogen bonds : angle 7.50066 ( 258) SS BOND : bond 0.00418 ( 15) SS BOND : angle 1.59105 ( 30) covalent geometry : bond 0.00324 ( 6172) covalent geometry : angle 0.87475 ( 8363) ********************** 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 182 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.6684 (pmm) cc_final: 0.6316 (mpp) REVERT: A 83 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6951 (mtt-85) REVERT: A 86 ARG cc_start: 0.7650 (mtm110) cc_final: 0.7395 (mtp180) REVERT: A 102 LYS cc_start: 0.7879 (mmtt) cc_final: 0.7573 (mmtt) REVERT: A 148 ASN cc_start: 0.8359 (t0) cc_final: 0.7513 (p0) REVERT: A 265 LYS cc_start: 0.8278 (tppt) cc_final: 0.7716 (tmtt) REVERT: A 313 HIS cc_start: 0.2796 (OUTLIER) cc_final: 0.2248 (t-90) REVERT: A 357 ASN cc_start: 0.7951 (t0) cc_final: 0.7632 (t0) REVERT: A 362 GLU cc_start: 0.6599 (mm-30) cc_final: 0.6281 (mm-30) REVERT: A 383 ARG cc_start: 0.8430 (mtt180) cc_final: 0.7998 (mtm110) REVERT: A 386 ARG cc_start: 0.7903 (mtt180) cc_final: 0.7521 (mtt180) REVERT: A 411 LEU cc_start: 0.8545 (mm) cc_final: 0.8244 (mp) REVERT: A 425 LYS cc_start: 0.7489 (mptt) cc_final: 0.7198 (mtpt) REVERT: A 465 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7333 (mp10) REVERT: A 482 PHE cc_start: 0.0566 (OUTLIER) cc_final: 0.0219 (t80) REVERT: A 500 LEU cc_start: 0.8041 (pp) cc_final: 0.7783 (tt) REVERT: A 514 ASN cc_start: 0.7902 (t0) cc_final: 0.7496 (t0) REVERT: C 504 MET cc_start: 0.7087 (mpp) cc_final: 0.6756 (mpp) REVERT: C 551 TRP cc_start: 0.7530 (t-100) cc_final: 0.7152 (t-100) REVERT: C 559 TRP cc_start: 0.0840 (OUTLIER) cc_final: -0.3059 (m-10) REVERT: C 587 TYR cc_start: 0.6561 (OUTLIER) cc_final: 0.5593 (m-80) REVERT: C 591 ASP cc_start: 0.5484 (t0) cc_final: 0.5166 (t0) outliers start: 36 outliers final: 28 residues processed: 169 average time/residue: 0.2081 time to fit residues: 44.7887 Evaluate side-chains 172 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 83 ARG 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 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 532 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 560 THR 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 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 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: 6.9990 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 61 optimal weight: 0.0970 chunk 31 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 7 optimal weight: 0.0770 chunk 41 optimal weight: 3.9990 overall best weight: 1.8342 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4360 r_free = 0.4360 target = 0.164282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.144802 restraints weight = 16278.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.149167 restraints weight = 10787.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.151880 restraints weight = 6490.013| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 6187 Z= 0.187 Angle : 0.907 14.435 8393 Z= 0.444 Chirality : 0.052 0.249 905 Planarity : 0.006 0.079 1070 Dihedral : 6.416 33.308 805 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 21.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.33 % Favored : 85.67 % Rotamer: Outliers : 6.05 % Allowed : 29.50 % Favored : 64.45 % 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: -3.38 (0.30), residues: 719 helix: -2.19 (0.49), residues: 96 sheet: -1.30 (0.62), residues: 77 loop : -2.62 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 551 HIS 0.010 0.002 HIS D 10 PHE 0.018 0.002 PHE A 39 TYR 0.024 0.002 TYR D 16 ARG 0.006 0.001 ARG A 65 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 101) hydrogen bonds : angle 7.83324 ( 258) SS BOND : bond 0.00480 ( 15) SS BOND : angle 1.61470 ( 30) covalent geometry : bond 0.00441 ( 6172) covalent geometry : angle 0.90360 ( 8363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2764.11 seconds wall clock time: 51 minutes 0.09 seconds (3060.09 seconds total)