Starting phenix.real_space_refine on Fri Dec 27 16:58:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bw8_30230/12_2024/7bw8_30230.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bw8_30230/12_2024/7bw8_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_30230/12_2024/7bw8_30230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bw8_30230/12_2024/7bw8_30230.map" model { file = "/net/cci-nas-00/data/ceres_data/7bw8_30230/12_2024/7bw8_30230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bw8_30230/12_2024/7bw8_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-5532/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: 3.94, per 1000 atoms: 0.65 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: 1.60 Conformation dependent library (CDL) restraints added in 876.0 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: 0.71 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: 1.43 Time building geometry restraints manager: 1.85 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: 0.220 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 17.680 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: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 6172 Z= 0.623 Angle : 1.376 12.295 8363 Z= 0.789 Chirality : 0.071 0.294 905 Planarity : 0.008 0.061 1070 Dihedral : 17.387 89.796 2275 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 49.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.25 % Favored : 77.75 % Rotamer: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.01 (0.26), residues: 719 helix: -2.92 (0.42), residues: 92 sheet: -2.21 (0.53), residues: 80 loop : -3.94 (0.23), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP A 183 HIS 0.022 0.004 HIS A 264 PHE 0.038 0.005 PHE A 231 TYR 0.077 0.005 TYR D 16 ARG 0.021 0.002 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.735 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: 0.2396 time to fit residues: 47.8070 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 : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 chunk 18 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN D 4 GLN D 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6172 Z= 0.264 Angle : 0.936 10.211 8363 Z= 0.475 Chirality : 0.054 0.221 905 Planarity : 0.006 0.069 1070 Dihedral : 7.723 27.930 805 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.02 % Favored : 84.98 % Rotamer: Outliers : 2.80 % Allowed : 16.67 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.58 (0.27), residues: 719 helix: -2.61 (0.45), residues: 96 sheet: -2.55 (0.44), residues: 106 loop : -3.52 (0.24), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 551 HIS 0.013 0.002 HIS A 264 PHE 0.017 0.002 PHE A 506 TYR 0.043 0.002 TYR D 16 ARG 0.006 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.6283 (pmm) cc_final: 0.5798 (pmm) REVERT: A 102 LYS cc_start: 0.8608 (pttm) cc_final: 0.8390 (mmtp) REVERT: A 383 ARG cc_start: 0.8281 (mtt180) cc_final: 0.7813 (mtm110) REVERT: A 465 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7322 (mp10) REVERT: C 572 PHE cc_start: 0.8923 (m-80) cc_final: 0.8718 (m-80) REVERT: C 591 ASP cc_start: 0.5222 (t0) cc_final: 0.4733 (t0) REVERT: D 13 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8266 (mt-10) REVERT: D 76 ASN cc_start: 0.7916 (m-40) cc_final: 0.6983 (m-40) outliers start: 19 outliers final: 14 residues processed: 174 average time/residue: 0.2130 time to fit residues: 46.4972 Evaluate side-chains 168 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain D residue 27 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 0.0370 chunk 22 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6172 Z= 0.207 Angle : 0.815 9.146 8363 Z= 0.409 Chirality : 0.050 0.210 905 Planarity : 0.006 0.058 1070 Dihedral : 6.793 24.123 805 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.63 % Favored : 86.37 % Rotamer: Outliers : 3.69 % Allowed : 21.53 % Favored : 74.78 % 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: -4.08 (0.28), residues: 719 helix: -2.33 (0.46), residues: 97 sheet: -2.03 (0.52), residues: 90 loop : -3.17 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 412 HIS 0.009 0.001 HIS A 264 PHE 0.018 0.002 PHE A 428 TYR 0.031 0.002 TYR D 16 ARG 0.007 0.001 ARG A 65 *********************** 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 182 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 383 ARG cc_start: 0.8319 (mtt180) cc_final: 0.7923 (mtm110) REVERT: A 465 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7307 (mp10) REVERT: A 500 LEU cc_start: 0.8144 (pp) cc_final: 0.7809 (tt) REVERT: C 591 ASP cc_start: 0.4936 (t0) cc_final: 0.4510 (t0) REVERT: D 13 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8269 (mt-10) outliers start: 25 outliers final: 19 residues processed: 167 average time/residue: 0.2138 time to fit residues: 45.0829 Evaluate side-chains 160 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 146 VAL 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 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 578 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 64 optimal weight: 4.9990 chunk 49 optimal weight: 0.0060 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6172 Z= 0.209 Angle : 0.775 9.367 8363 Z= 0.390 Chirality : 0.048 0.207 905 Planarity : 0.005 0.077 1070 Dihedral : 6.476 24.172 805 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.54 % Favored : 88.32 % Rotamer: Outliers : 5.46 % Allowed : 24.19 % Favored : 70.35 % 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: -3.73 (0.29), residues: 719 helix: -2.00 (0.50), residues: 92 sheet: -1.97 (0.51), residues: 97 loop : -2.91 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 251 HIS 0.008 0.001 HIS D 10 PHE 0.012 0.002 PHE A 258 TYR 0.024 0.001 TYR D 16 ARG 0.008 0.001 ARG A 83 *********************** 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 184 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.6869 (pmm) cc_final: 0.6572 (pmm) REVERT: A 65 ARG cc_start: 0.6933 (ttm-80) cc_final: 0.6651 (tpp-160) REVERT: A 83 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7187 (mtp180) REVERT: A 313 HIS cc_start: 0.3248 (OUTLIER) cc_final: 0.1431 (m-70) REVERT: A 383 ARG cc_start: 0.8324 (mtt180) cc_final: 0.7908 (mtm110) REVERT: A 465 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7313 (mp10) REVERT: A 482 PHE cc_start: 0.0675 (OUTLIER) cc_final: 0.0316 (t80) REVERT: A 488 ARG cc_start: 0.6597 (mmm-85) cc_final: 0.6242 (mmm-85) REVERT: A 500 LEU cc_start: 0.8140 (pp) cc_final: 0.7881 (tt) REVERT: C 591 ASP cc_start: 0.4791 (t0) cc_final: 0.4447 (t0) outliers start: 37 outliers final: 26 residues processed: 167 average time/residue: 0.2366 time to fit residues: 50.6594 Evaluate side-chains 165 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 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 569 LEU Chi-restraints excluded: chain A residue 586 ILE 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 590 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 27 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 0.0770 chunk 59 optimal weight: 0.4980 chunk 48 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 17 optimal weight: 0.0370 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN C 546 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6172 Z= 0.191 Angle : 0.759 9.061 8363 Z= 0.379 Chirality : 0.048 0.187 905 Planarity : 0.005 0.053 1070 Dihedral : 6.118 21.457 805 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 4.72 % Allowed : 27.14 % Favored : 68.14 % 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: -3.53 (0.29), residues: 719 helix: -1.91 (0.51), residues: 93 sheet: -1.64 (0.54), residues: 93 loop : -2.78 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 251 HIS 0.005 0.001 HIS D 10 PHE 0.012 0.001 PHE A 39 TYR 0.023 0.001 TYR D 16 ARG 0.004 0.001 ARG A 86 *********************** 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 172 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8054 (mm-30) REVERT: A 11 MET cc_start: 0.6993 (pmm) cc_final: 0.6407 (pmm) REVERT: A 38 MET cc_start: 0.3273 (tpt) cc_final: 0.2960 (tpt) REVERT: A 65 ARG cc_start: 0.6909 (ttm-80) cc_final: 0.6610 (tpp-160) REVERT: A 83 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7160 (mtp180) REVERT: A 102 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7873 (mmtt) REVERT: A 125 LEU cc_start: 0.8303 (mt) cc_final: 0.8066 (mt) REVERT: A 265 LYS cc_start: 0.7411 (tmtt) cc_final: 0.7145 (tppt) REVERT: A 313 HIS cc_start: 0.3064 (OUTLIER) cc_final: 0.1239 (m-70) REVERT: A 383 ARG cc_start: 0.8288 (mtt180) cc_final: 0.7906 (mtm110) REVERT: A 465 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7225 (mp10) REVERT: A 482 PHE cc_start: 0.0486 (OUTLIER) cc_final: 0.0148 (t80) REVERT: A 551 TRP cc_start: 0.6093 (t-100) cc_final: 0.5751 (t-100) REVERT: C 587 TYR cc_start: 0.6714 (OUTLIER) cc_final: 0.5578 (m-80) REVERT: C 591 ASP cc_start: 0.4759 (t0) cc_final: 0.4495 (t0) REVERT: D 76 ASN cc_start: 0.8419 (m-40) cc_final: 0.7650 (m110) outliers start: 32 outliers final: 22 residues processed: 156 average time/residue: 0.2115 time to fit residues: 42.1576 Evaluate side-chains 158 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 251 TRP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 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 565 PHE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 572 PHE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 579 TYR Chi-restraints excluded: chain C residue 587 TYR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 27 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 100 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6172 Z= 0.225 Angle : 0.769 10.385 8363 Z= 0.386 Chirality : 0.049 0.188 905 Planarity : 0.005 0.081 1070 Dihedral : 6.169 28.836 805 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % Rotamer: Outliers : 5.60 % Allowed : 27.29 % Favored : 67.11 % 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: -3.57 (0.29), residues: 719 helix: -1.93 (0.51), residues: 94 sheet: -1.73 (0.54), residues: 93 loop : -2.80 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 551 HIS 0.012 0.001 HIS D 10 PHE 0.012 0.002 PHE C 565 TYR 0.024 0.002 TYR D 16 ARG 0.007 0.001 ARG A 86 *********************** 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 176 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8078 (mm-30) REVERT: A 11 MET cc_start: 0.6903 (pmm) cc_final: 0.6229 (pmm) REVERT: A 38 MET cc_start: 0.3534 (tpt) cc_final: 0.3172 (tpt) REVERT: A 83 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7139 (mtp180) REVERT: A 100 HIS cc_start: 0.5755 (OUTLIER) cc_final: 0.5346 (t70) REVERT: A 125 LEU cc_start: 0.8307 (mt) cc_final: 0.8068 (mt) REVERT: A 239 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8398 (mm-30) REVERT: A 313 HIS cc_start: 0.3185 (OUTLIER) cc_final: 0.1406 (m-70) REVERT: A 383 ARG cc_start: 0.8338 (mtt180) cc_final: 0.7989 (mtm110) REVERT: A 465 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7548 (mp10) REVERT: A 500 LEU cc_start: 0.8199 (pp) cc_final: 0.7888 (tt) REVERT: A 504 MET cc_start: 0.4480 (tpp) cc_final: 0.4016 (mmm) REVERT: C 551 TRP cc_start: 0.7555 (t-100) cc_final: 0.7219 (t-100) REVERT: C 559 TRP cc_start: 0.0453 (OUTLIER) cc_final: -0.3113 (m-10) REVERT: C 587 TYR cc_start: 0.6654 (OUTLIER) cc_final: 0.5684 (m-80) REVERT: C 591 ASP cc_start: 0.4901 (t0) cc_final: 0.4533 (t0) REVERT: C 695 GLU cc_start: 0.8476 (pm20) cc_final: 0.8201 (pm20) outliers start: 38 outliers final: 28 residues processed: 162 average time/residue: 0.2045 time to fit residues: 42.7920 Evaluate side-chains 168 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 201 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 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 532 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain C residue 559 TRP Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 572 PHE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 579 TYR Chi-restraints excluded: chain C residue 587 TYR Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 27 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 0.0570 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6172 Z= 0.194 Angle : 0.759 9.614 8363 Z= 0.377 Chirality : 0.049 0.209 905 Planarity : 0.005 0.076 1070 Dihedral : 6.028 25.235 805 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.10 % Favored : 87.90 % Rotamer: Outliers : 6.05 % Allowed : 28.17 % Favored : 65.78 % 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: -1.69 (0.52), residues: 94 sheet: -1.58 (0.57), residues: 87 loop : -2.65 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 551 HIS 0.011 0.001 HIS D 10 PHE 0.018 0.001 PHE A 428 TYR 0.026 0.001 TYR D 16 ARG 0.005 0.001 ARG A 86 *********************** 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 184 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8028 (mm-30) REVERT: A 11 MET cc_start: 0.6697 (pmm) cc_final: 0.5992 (pmm) REVERT: A 83 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7021 (mtp180) REVERT: A 102 LYS cc_start: 0.8032 (mmtp) cc_final: 0.7806 (mmtt) REVERT: A 239 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8242 (mm-30) REVERT: A 265 LYS cc_start: 0.7472 (tmtt) cc_final: 0.7229 (tppt) REVERT: A 313 HIS cc_start: 0.3029 (OUTLIER) cc_final: 0.1231 (m-70) REVERT: A 357 ASN cc_start: 0.7799 (t0) cc_final: 0.7479 (t0) REVERT: A 383 ARG cc_start: 0.8313 (mtt180) cc_final: 0.7965 (mtm110) REVERT: A 482 PHE cc_start: 0.0687 (OUTLIER) cc_final: 0.0300 (t80) REVERT: A 500 LEU cc_start: 0.8172 (pp) cc_final: 0.7848 (tt) REVERT: C 551 TRP cc_start: 0.7564 (t-100) cc_final: 0.7159 (t-100) REVERT: C 559 TRP cc_start: 0.0386 (OUTLIER) cc_final: -0.3236 (m-10) REVERT: C 572 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8585 (t80) REVERT: C 587 TYR cc_start: 0.6546 (OUTLIER) cc_final: 0.5605 (m-80) REVERT: C 591 ASP cc_start: 0.4908 (t0) cc_final: 0.4556 (t0) REVERT: C 695 GLU cc_start: 0.8465 (pm20) cc_final: 0.8242 (pm20) REVERT: D 76 ASN cc_start: 0.7864 (OUTLIER) cc_final: 0.7482 (t0) outliers start: 41 outliers final: 27 residues processed: 170 average time/residue: 0.1957 time to fit residues: 42.6020 Evaluate side-chains 166 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 79 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 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 478 ILE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 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 C residue 559 TRP Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 572 PHE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 579 TYR Chi-restraints excluded: chain C residue 587 TYR Chi-restraints excluded: chain C residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.0870 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6172 Z= 0.188 Angle : 0.785 10.485 8363 Z= 0.384 Chirality : 0.049 0.217 905 Planarity : 0.005 0.068 1070 Dihedral : 5.934 22.712 805 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % Rotamer: Outliers : 5.75 % Allowed : 29.06 % Favored : 65.19 % 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: -3.24 (0.30), residues: 719 helix: -1.62 (0.54), residues: 94 sheet: -1.45 (0.59), residues: 84 loop : -2.58 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 551 HIS 0.010 0.001 HIS D 10 PHE 0.016 0.001 PHE A 428 TYR 0.025 0.002 TYR C 507 ARG 0.008 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8075 (mm-30) REVERT: A 38 MET cc_start: 0.3342 (tpt) cc_final: 0.3091 (tpt) REVERT: A 83 ARG cc_start: 0.7548 (mtp180) cc_final: 0.7068 (mtp180) REVERT: A 148 ASN cc_start: 0.8326 (t0) cc_final: 0.7826 (p0) REVERT: A 265 LYS cc_start: 0.7459 (tmtt) cc_final: 0.7253 (tppt) REVERT: A 313 HIS cc_start: 0.2848 (OUTLIER) cc_final: 0.2394 (t-90) REVERT: A 383 ARG cc_start: 0.8300 (mtt180) cc_final: 0.7948 (mtm110) REVERT: A 482 PHE cc_start: 0.0675 (OUTLIER) cc_final: 0.0371 (t80) REVERT: A 500 LEU cc_start: 0.8104 (pp) cc_final: 0.7840 (tt) REVERT: A 504 MET cc_start: 0.4115 (mmm) cc_final: 0.3275 (mmm) REVERT: A 551 TRP cc_start: 0.5942 (t-100) cc_final: 0.5173 (t-100) REVERT: A 553 MET cc_start: 0.7394 (mmm) cc_final: 0.7052 (mmm) REVERT: A 560 THR cc_start: 0.3580 (OUTLIER) cc_final: 0.3106 (p) REVERT: C 551 TRP cc_start: 0.7512 (t-100) cc_final: 0.7162 (t-100) REVERT: C 567 LYS cc_start: 0.3402 (ttmt) cc_final: 0.3171 (tttt) REVERT: C 572 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8638 (t80) REVERT: C 587 TYR cc_start: 0.6560 (OUTLIER) cc_final: 0.5624 (m-80) REVERT: C 591 ASP cc_start: 0.5051 (t0) cc_final: 0.4755 (t0) REVERT: D 76 ASN cc_start: 0.7868 (OUTLIER) cc_final: 0.7529 (t0) outliers start: 39 outliers final: 26 residues processed: 169 average time/residue: 0.2087 time to fit residues: 45.3755 Evaluate side-chains 166 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 81 VAL 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 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 474 LYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 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 C residue 570 VAL Chi-restraints excluded: chain C residue 572 PHE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 579 TYR Chi-restraints excluded: chain C residue 587 TYR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 76 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6172 Z= 0.264 Angle : 0.843 12.839 8363 Z= 0.420 Chirality : 0.051 0.216 905 Planarity : 0.005 0.073 1070 Dihedral : 6.169 29.755 805 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.80 % Favored : 87.20 % Rotamer: Outliers : 5.46 % Allowed : 30.09 % Favored : 64.45 % 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: -3.41 (0.29), residues: 719 helix: -1.76 (0.52), residues: 94 sheet: -1.57 (0.57), residues: 82 loop : -2.70 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 551 HIS 0.009 0.001 HIS D 10 PHE 0.016 0.002 PHE A 39 TYR 0.029 0.002 TYR D 16 ARG 0.009 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8109 (mm-30) REVERT: A 11 MET cc_start: 0.6710 (pmm) cc_final: 0.6501 (pmm) REVERT: A 83 ARG cc_start: 0.7610 (mtp180) cc_final: 0.7151 (mtp180) REVERT: A 102 LYS cc_start: 0.7882 (mmtt) cc_final: 0.7592 (mmtt) REVERT: A 148 ASN cc_start: 0.8398 (t0) cc_final: 0.7622 (p0) REVERT: A 313 HIS cc_start: 0.3181 (OUTLIER) cc_final: 0.2659 (t-90) REVERT: A 383 ARG cc_start: 0.8385 (mtt180) cc_final: 0.8026 (mtm110) REVERT: A 465 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7362 (mp10) REVERT: A 504 MET cc_start: 0.3665 (mmm) cc_final: 0.2940 (mmm) REVERT: C 551 TRP cc_start: 0.7650 (t-100) cc_final: 0.7336 (t-100) REVERT: C 559 TRP cc_start: 0.0052 (OUTLIER) cc_final: -0.3315 (m-10) REVERT: C 572 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8706 (t80) REVERT: C 587 TYR cc_start: 0.6652 (OUTLIER) cc_final: 0.5705 (m-80) REVERT: C 591 ASP cc_start: 0.5134 (t0) cc_final: 0.4689 (t0) REVERT: D 76 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7716 (t0) outliers start: 37 outliers final: 25 residues processed: 164 average time/residue: 0.2112 time to fit residues: 43.6287 Evaluate side-chains 169 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 79 LEU 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 507 TYR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 0.0870 chunk 45 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- 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 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6172 Z= 0.295 Angle : 0.903 13.661 8363 Z= 0.448 Chirality : 0.053 0.231 905 Planarity : 0.006 0.076 1070 Dihedral : 6.505 33.165 805 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.91 % Favored : 86.09 % Rotamer: Outliers : 5.16 % Allowed : 30.09 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.29), residues: 719 helix: -1.93 (0.50), residues: 96 sheet: -1.70 (0.56), residues: 85 loop : -2.78 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP A 551 HIS 0.011 0.002 HIS D 10 PHE 0.014 0.002 PHE A 381 TYR 0.031 0.002 TYR D 16 ARG 0.010 0.001 ARG A 135 ********************** 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 171 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8086 (mm-30) REVERT: A 11 MET cc_start: 0.6319 (pmm) cc_final: 0.5602 (pmm) REVERT: A 83 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7141 (mtp180) REVERT: A 98 MET cc_start: 0.5460 (tpp) cc_final: 0.4956 (tpp) REVERT: A 102 LYS cc_start: 0.7758 (mmtt) cc_final: 0.7521 (mmtt) REVERT: A 313 HIS cc_start: 0.3238 (OUTLIER) cc_final: 0.2717 (t-90) REVERT: A 362 GLU cc_start: 0.6404 (mm-30) cc_final: 0.6021 (mm-30) REVERT: A 383 ARG cc_start: 0.8386 (mtt180) cc_final: 0.8018 (mtm110) REVERT: A 386 ARG cc_start: 0.7797 (mtt180) cc_final: 0.7343 (mtt180) REVERT: A 465 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7434 (mp10) REVERT: A 500 LEU cc_start: 0.7792 (pp) cc_final: 0.7565 (tt) REVERT: A 504 MET cc_start: 0.3397 (mmm) cc_final: 0.2746 (mmm) REVERT: C 488 ARG cc_start: 0.8142 (tpt170) cc_final: 0.7710 (ttt90) REVERT: C 551 TRP cc_start: 0.7804 (t-100) cc_final: 0.7486 (t-100) REVERT: C 559 TRP cc_start: 0.0192 (OUTLIER) cc_final: -0.3211 (m-10) REVERT: C 587 TYR cc_start: 0.6629 (OUTLIER) cc_final: 0.6049 (m-80) REVERT: C 591 ASP cc_start: 0.5869 (t0) cc_final: 0.5452 (t0) REVERT: C 695 GLU cc_start: 0.8619 (pm20) cc_final: 0.8203 (pm20) REVERT: D 76 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7937 (t0) outliers start: 35 outliers final: 27 residues processed: 157 average time/residue: 0.2146 time to fit residues: 42.5048 Evaluate side-chains 164 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 79 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 251 TRP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain 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 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 52 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 0.0050 chunk 3 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- 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 = 0.4380 r_free = 0.4380 target = 0.167540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.148831 restraints weight = 16137.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.152955 restraints weight = 10224.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.156170 restraints weight = 6221.932| |-----------------------------------------------------------------------------| r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6172 Z= 0.241 Angle : 0.877 13.453 8363 Z= 0.430 Chirality : 0.052 0.220 905 Planarity : 0.005 0.069 1070 Dihedral : 6.316 27.668 805 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.49 % Favored : 86.51 % Rotamer: Outliers : 4.57 % Allowed : 31.12 % 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: -3.50 (0.29), residues: 719 helix: -2.07 (0.49), residues: 98 sheet: -1.58 (0.63), residues: 70 loop : -2.72 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 551 HIS 0.010 0.001 HIS D 10 PHE 0.019 0.002 PHE A 258 TYR 0.028 0.002 TYR D 16 ARG 0.005 0.001 ARG A 554 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1731.67 seconds wall clock time: 32 minutes 13.39 seconds (1933.39 seconds total)