Starting phenix.real_space_refine on Tue Feb 11 14:27:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yhu_39301/02_2025/8yhu_39301.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yhu_39301/02_2025/8yhu_39301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yhu_39301/02_2025/8yhu_39301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yhu_39301/02_2025/8yhu_39301.map" model { file = "/net/cci-nas-00/data/ceres_data/8yhu_39301/02_2025/8yhu_39301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yhu_39301/02_2025/8yhu_39301.cif" } resolution = 2.88 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= 0.001 sd= 0.022 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 19 5.16 5 C 3805 2.51 5 N 998 2.21 5 O 1168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5990 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5323 Classifications: {'peptide': 663} Link IDs: {'PTRANS': 26, 'TRANS': 636} Chain breaks: 1 Chain: "B" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 457 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.57, per 1000 atoms: 0.76 Number of scatterers: 5990 At special positions: 0 Unit cell: (56.44, 103.584, 112.216, 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 19 16.00 O 1168 8.00 N 998 7.00 C 3805 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 37 " distance=2.03 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 122 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 677 " distance=2.03 Simple disulfide: pdb=" SG CYS A 651 " - pdb=" SG CYS A 696 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A 801 " - " ASN A 57 " " NAG A 802 " - " ASN A 124 " " NAG A 803 " - " ASN A 252 " " NAG A 804 " - " ASN A 275 " " NAG A 805 " - " ASN A 291 " " NAG C 1 " - " ASN A 52 " " NAG D 1 " - " ASN A 247 " " NAG E 1 " - " ASN A 265 " " NAG F 1 " - " ASN A 398 " " NAG G 1 " - " ASN A 413 " Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 826.7 milliseconds 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 8 sheets defined 15.3% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.556A pdb=" N THR A 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 73 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.592A pdb=" N GLN A 96 " --> pdb=" O PRO A 92 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 92 through 97' Processing helix chain 'A' and resid 188 through 195 removed outlier: 5.162A pdb=" N ILE A 193 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 245 removed outlier: 3.796A pdb=" N LEU A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.693A pdb=" N TRP A 273 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 449 through 453 removed outlier: 3.697A pdb=" N TRP A 452 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG A 453 " --> pdb=" O GLN A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 449 through 453' Processing helix chain 'A' and resid 542 through 547 removed outlier: 3.948A pdb=" N TRP A 546 " --> pdb=" O ALA A 543 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 547 " --> pdb=" O ARG A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 692 through 696 removed outlier: 3.564A pdb=" N SER A 695 " --> pdb=" O ASP A 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 4 Processing helix chain 'B' and resid 5 through 17 removed outlier: 3.892A pdb=" N VAL B 9 " --> pdb=" O GLU B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 38 Processing helix chain 'B' and resid 43 through 54 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 4.367A pdb=" N THR A 29 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 56 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP A 81 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LEU A 80 " --> pdb=" O ASN A 105 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 104 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU A 128 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 152 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 199 removed outlier: 6.076A pdb=" N ARG A 222 " --> pdb=" O LEU A 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 302 through 304 removed outlier: 7.699A pdb=" N PHE A 303 " --> pdb=" O ASN A 328 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396 removed outlier: 3.508A pdb=" N LEU A 396 " --> pdb=" O LYS A 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 411 through 412 Processing sheet with id=AA6, first strand: chain 'A' and resid 444 through 446 removed outlier: 3.605A pdb=" N GLN A 470 " --> pdb=" O GLN A 445 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 461 through 462 removed outlier: 3.546A pdb=" N MET A 486 " --> pdb=" O ILE A 461 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 615 through 616 removed outlier: 7.880A pdb=" N LEU A 615 " --> pdb=" O ASP A 641 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 59 hydrogen bonds defined for protein. 141 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: 1.59 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1934 1.34 - 1.46: 1153 1.46 - 1.58: 2990 1.58 - 1.69: 0 1.69 - 1.81: 27 Bond restraints: 6104 Sorted by residual: bond pdb=" N GLY A 594 " pdb=" CA GLY A 594 " ideal model delta sigma weight residual 1.447 1.475 -0.028 9.30e-03 1.16e+04 9.12e+00 bond pdb=" N ILE A 622 " pdb=" CA ILE A 622 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.24e-02 6.50e+03 8.07e+00 bond pdb=" N ASN A 596 " pdb=" CA ASN A 596 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.24e-02 6.50e+03 5.91e+00 bond pdb=" N LEU A 621 " pdb=" CA LEU A 621 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.22e-02 6.72e+03 5.30e+00 bond pdb=" N ASN A 620 " pdb=" CA ASN A 620 " ideal model delta sigma weight residual 1.451 1.486 -0.034 1.62e-02 3.81e+03 4.48e+00 ... (remaining 6099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 7724 1.32 - 2.64: 437 2.64 - 3.96: 88 3.96 - 5.27: 25 5.27 - 6.59: 4 Bond angle restraints: 8278 Sorted by residual: angle pdb=" N ASN A 124 " pdb=" CA ASN A 124 " pdb=" C ASN A 124 " ideal model delta sigma weight residual 111.71 107.09 4.62 1.34e+00 5.57e-01 1.19e+01 angle pdb=" N GLN A 62 " pdb=" CA GLN A 62 " pdb=" C GLN A 62 " ideal model delta sigma weight residual 110.80 117.39 -6.59 2.13e+00 2.20e-01 9.58e+00 angle pdb=" CA GLY A 594 " pdb=" C GLY A 594 " pdb=" O GLY A 594 " ideal model delta sigma weight residual 121.31 118.17 3.14 1.09e+00 8.42e-01 8.31e+00 angle pdb=" C VAL A 144 " pdb=" N LYS A 145 " pdb=" CA LYS A 145 " ideal model delta sigma weight residual 121.71 117.82 3.89 1.39e+00 5.18e-01 7.85e+00 angle pdb=" CA LEU A 595 " pdb=" C LEU A 595 " pdb=" O LEU A 595 " ideal model delta sigma weight residual 121.54 118.33 3.21 1.16e+00 7.43e-01 7.64e+00 ... (remaining 8273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.19: 3552 21.19 - 42.38: 291 42.38 - 63.57: 37 63.57 - 84.76: 9 84.76 - 105.96: 8 Dihedral angle restraints: 3897 sinusoidal: 1779 harmonic: 2118 Sorted by residual: dihedral pdb=" CB CYS A 651 " pdb=" SG CYS A 651 " pdb=" SG CYS A 696 " pdb=" CB CYS A 696 " ideal model delta sinusoidal sigma weight residual 93.00 28.29 64.71 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" CB CYS A 649 " pdb=" SG CYS A 649 " pdb=" SG CYS A 677 " pdb=" CB CYS A 677 " ideal model delta sinusoidal sigma weight residual 93.00 50.31 42.69 1 1.00e+01 1.00e-02 2.54e+01 dihedral pdb=" CA HIS A 60 " pdb=" C HIS A 60 " pdb=" N ASN A 61 " pdb=" CA ASN A 61 " ideal model delta harmonic sigma weight residual -180.00 -158.21 -21.79 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 3894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 912 0.085 - 0.170: 84 0.170 - 0.256: 6 0.256 - 0.341: 1 0.341 - 0.426: 1 Chirality restraints: 1004 Sorted by residual: chirality pdb=" C1 NAG A 804 " pdb=" ND2 ASN A 275 " pdb=" C2 NAG A 804 " pdb=" O5 NAG A 804 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CA GLN A 62 " pdb=" N GLN A 62 " pdb=" C GLN A 62 " pdb=" CB GLN A 62 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C1 NAG A 805 " pdb=" ND2 ASN A 291 " pdb=" C2 NAG A 805 " pdb=" O5 NAG A 805 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1001 not shown) Planarity restraints: 1051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 303 " -0.021 2.00e-02 2.50e+03 1.70e-02 5.07e+00 pdb=" CG PHE A 303 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 303 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 303 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 303 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 303 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 303 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 297 " 0.033 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO A 298 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 298 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 298 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 645 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO A 646 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 646 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 646 " -0.024 5.00e-02 4.00e+02 ... (remaining 1048 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1242 2.78 - 3.31: 5735 3.31 - 3.84: 9412 3.84 - 4.37: 11243 4.37 - 4.90: 18707 Nonbonded interactions: 46339 Sorted by model distance: nonbonded pdb=" OG SER A 500 " pdb=" O ASP A 524 " model vdw 2.248 3.040 nonbonded pdb=" O ASP A 648 " pdb=" OG SER A 653 " model vdw 2.252 3.040 nonbonded pdb=" O THR A 248 " pdb=" OG1 THR A 274 " model vdw 2.275 3.040 nonbonded pdb=" O ASN A 85 " pdb=" ND2 ASN A 109 " model vdw 2.285 3.120 nonbonded pdb=" OD1 ASP A 366 " pdb=" OG1 THR A 391 " model vdw 2.290 3.040 ... (remaining 46334 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 17.680 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:13.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 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 : 0.004 0.035 6104 Z= 0.262 Angle : 0.718 6.594 8278 Z= 0.369 Chirality : 0.052 0.426 1004 Planarity : 0.004 0.051 1041 Dihedral : 15.503 105.956 2497 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.04 % Favored : 86.82 % Rotamer: Outliers : 0.30 % Allowed : 0.30 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.42 (0.31), residues: 713 helix: -0.83 (0.61), residues: 72 sheet: -3.97 (0.53), residues: 75 loop : -2.43 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 546 HIS 0.003 0.001 HIS A 60 PHE 0.038 0.002 PHE A 303 TYR 0.008 0.001 TYR A 283 ARG 0.004 0.000 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 119 PHE cc_start: 0.6524 (p90) cc_final: 0.5817 (p90) REVERT: A 621 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5813 (mm) outliers start: 2 outliers final: 1 residues processed: 101 average time/residue: 0.9076 time to fit residues: 97.7977 Evaluate side-chains 88 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 621 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 328 ASN A 361 ASN A 540 ASN A 609 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.175830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.154467 restraints weight = 8031.764| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.74 r_work: 0.4048 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6104 Z= 0.292 Angle : 0.726 9.301 8278 Z= 0.356 Chirality : 0.051 0.397 1004 Planarity : 0.004 0.045 1041 Dihedral : 10.887 81.600 1074 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 1.80 % Allowed : 10.04 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.45 (0.31), residues: 713 helix: -0.85 (0.59), residues: 74 sheet: -4.33 (0.50), residues: 78 loop : -2.39 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 296 HIS 0.004 0.001 HIS A 359 PHE 0.029 0.002 PHE A 557 TYR 0.012 0.002 TYR A 675 ARG 0.004 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 103 VAL cc_start: 0.8060 (p) cc_final: 0.7824 (t) REVERT: A 119 PHE cc_start: 0.6679 (p90) cc_final: 0.5914 (p90) REVERT: A 363 GLU cc_start: 0.6324 (tp30) cc_final: 0.6086 (tp30) REVERT: A 418 LYS cc_start: 0.7986 (mppt) cc_final: 0.7781 (mppt) REVERT: A 531 LYS cc_start: 0.7115 (pttp) cc_final: 0.6772 (pttp) REVERT: A 626 GLU cc_start: 0.6581 (pp20) cc_final: 0.6321 (pp20) outliers start: 12 outliers final: 5 residues processed: 102 average time/residue: 0.8626 time to fit residues: 94.1810 Evaluate side-chains 94 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 625 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 207 ASN A 328 ASN A 361 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.174583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.153394 restraints weight = 8119.133| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.72 r_work: 0.4028 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6104 Z= 0.344 Angle : 0.722 9.386 8278 Z= 0.358 Chirality : 0.051 0.388 1004 Planarity : 0.004 0.043 1041 Dihedral : 9.284 58.694 1070 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.74 % Favored : 86.26 % Rotamer: Outliers : 2.70 % Allowed : 13.19 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.30), residues: 713 helix: -0.77 (0.59), residues: 74 sheet: -4.48 (0.50), residues: 73 loop : -2.48 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 296 HIS 0.004 0.001 HIS A 359 PHE 0.033 0.002 PHE A 557 TYR 0.012 0.002 TYR A 675 ARG 0.002 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 VAL cc_start: 0.8071 (OUTLIER) cc_final: 0.7840 (t) REVERT: A 119 PHE cc_start: 0.6739 (p90) cc_final: 0.5967 (p90) REVERT: A 363 GLU cc_start: 0.6334 (tp30) cc_final: 0.6073 (tp30) REVERT: A 486 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6251 (mmm) REVERT: A 531 LYS cc_start: 0.7221 (pttp) cc_final: 0.6854 (pttp) outliers start: 18 outliers final: 9 residues processed: 102 average time/residue: 0.8135 time to fit residues: 88.9764 Evaluate side-chains 97 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 675 TYR Chi-restraints excluded: chain A residue 695 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.174430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.153330 restraints weight = 8188.273| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 2.73 r_work: 0.4027 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6104 Z= 0.325 Angle : 0.721 9.395 8278 Z= 0.355 Chirality : 0.051 0.383 1004 Planarity : 0.004 0.042 1041 Dihedral : 8.211 55.723 1070 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.18 % Favored : 86.82 % Rotamer: Outliers : 2.85 % Allowed : 14.84 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.55 (0.30), residues: 713 helix: -0.68 (0.60), residues: 74 sheet: -4.62 (0.48), residues: 73 loop : -2.49 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 296 HIS 0.005 0.001 HIS A 359 PHE 0.032 0.002 PHE A 557 TYR 0.010 0.002 TYR A 675 ARG 0.002 0.000 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 VAL cc_start: 0.8067 (OUTLIER) cc_final: 0.7827 (t) REVERT: A 119 PHE cc_start: 0.6767 (p90) cc_final: 0.5958 (p90) REVERT: A 150 ILE cc_start: 0.5852 (OUTLIER) cc_final: 0.5622 (mp) REVERT: A 381 LEU cc_start: 0.7392 (tp) cc_final: 0.7093 (tt) REVERT: A 486 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6189 (mmm) REVERT: A 626 GLU cc_start: 0.6618 (pp20) cc_final: 0.6297 (pp20) outliers start: 19 outliers final: 10 residues processed: 103 average time/residue: 0.8409 time to fit residues: 92.7280 Evaluate side-chains 96 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 675 TYR Chi-restraints excluded: chain A residue 695 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 26 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.175766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.154604 restraints weight = 8151.712| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.75 r_work: 0.4047 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6104 Z= 0.224 Angle : 0.658 9.389 8278 Z= 0.326 Chirality : 0.049 0.387 1004 Planarity : 0.004 0.044 1041 Dihedral : 7.576 55.885 1070 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.76 % Favored : 87.24 % Rotamer: Outliers : 3.00 % Allowed : 15.59 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.42 (0.30), residues: 713 helix: -0.48 (0.60), residues: 74 sheet: -4.54 (0.50), residues: 73 loop : -2.41 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 296 HIS 0.003 0.001 HIS A 539 PHE 0.021 0.001 PHE A 557 TYR 0.008 0.001 TYR A 383 ARG 0.002 0.000 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 VAL cc_start: 0.8063 (OUTLIER) cc_final: 0.7814 (t) REVERT: A 119 PHE cc_start: 0.6746 (p90) cc_final: 0.5917 (p90) REVERT: A 150 ILE cc_start: 0.5882 (OUTLIER) cc_final: 0.5650 (mp) REVERT: A 363 GLU cc_start: 0.6385 (tp30) cc_final: 0.6082 (tp30) outliers start: 20 outliers final: 10 residues processed: 103 average time/residue: 0.8685 time to fit residues: 96.2102 Evaluate side-chains 97 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 621 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 65 optimal weight: 4.9990 chunk 48 optimal weight: 0.1980 chunk 63 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.175970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.155073 restraints weight = 8019.900| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 2.70 r_work: 0.4051 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6104 Z= 0.235 Angle : 0.675 10.672 8278 Z= 0.328 Chirality : 0.049 0.389 1004 Planarity : 0.004 0.042 1041 Dihedral : 7.295 55.856 1070 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 3.30 % Allowed : 16.49 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.39 (0.30), residues: 713 helix: -0.58 (0.59), residues: 74 sheet: -4.39 (0.56), residues: 63 loop : -2.44 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 452 HIS 0.004 0.001 HIS A 359 PHE 0.024 0.001 PHE A 557 TYR 0.007 0.001 TYR A 383 ARG 0.001 0.000 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7805 (t) REVERT: A 119 PHE cc_start: 0.6751 (p90) cc_final: 0.5916 (p90) REVERT: A 150 ILE cc_start: 0.5855 (OUTLIER) cc_final: 0.5608 (mp) REVERT: A 363 GLU cc_start: 0.6351 (tp30) cc_final: 0.6026 (tp30) REVERT: A 418 LYS cc_start: 0.8023 (mppt) cc_final: 0.7821 (mppt) REVERT: A 437 ASP cc_start: 0.5636 (OUTLIER) cc_final: 0.5411 (t70) outliers start: 22 outliers final: 12 residues processed: 103 average time/residue: 0.7850 time to fit residues: 86.7216 Evaluate side-chains 96 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 675 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 56 optimal weight: 0.0870 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.175274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.154234 restraints weight = 8112.135| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 2.73 r_work: 0.4039 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6104 Z= 0.269 Angle : 0.680 9.406 8278 Z= 0.337 Chirality : 0.050 0.394 1004 Planarity : 0.004 0.044 1041 Dihedral : 7.185 55.852 1070 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.76 % Favored : 87.24 % Rotamer: Outliers : 3.60 % Allowed : 16.79 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.40 (0.30), residues: 713 helix: -0.58 (0.59), residues: 74 sheet: -4.48 (0.55), residues: 63 loop : -2.45 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 296 HIS 0.004 0.001 HIS A 359 PHE 0.028 0.002 PHE A 557 TYR 0.008 0.001 TYR A 675 ARG 0.002 0.000 ARG A 643 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7815 (t) REVERT: A 119 PHE cc_start: 0.6785 (p90) cc_final: 0.5940 (p90) REVERT: A 150 ILE cc_start: 0.5845 (OUTLIER) cc_final: 0.5598 (mp) REVERT: A 363 GLU cc_start: 0.6355 (tp30) cc_final: 0.6023 (tp30) REVERT: A 418 LYS cc_start: 0.8045 (mppt) cc_final: 0.7838 (mppt) REVERT: A 437 ASP cc_start: 0.5657 (OUTLIER) cc_final: 0.5426 (t70) REVERT: A 626 GLU cc_start: 0.6600 (pp20) cc_final: 0.6320 (pp20) outliers start: 24 outliers final: 14 residues processed: 102 average time/residue: 0.8704 time to fit residues: 94.8858 Evaluate side-chains 100 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 675 TYR Chi-restraints excluded: chain A residue 695 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 52 optimal weight: 0.0270 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.176664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.155577 restraints weight = 8059.528| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.70 r_work: 0.4055 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6104 Z= 0.204 Angle : 0.647 9.421 8278 Z= 0.318 Chirality : 0.048 0.396 1004 Planarity : 0.004 0.043 1041 Dihedral : 6.981 55.999 1070 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.34 % Favored : 87.66 % Rotamer: Outliers : 3.15 % Allowed : 18.59 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.30 (0.30), residues: 713 helix: -0.46 (0.59), residues: 74 sheet: -4.34 (0.56), residues: 63 loop : -2.39 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 452 HIS 0.003 0.001 HIS A 359 PHE 0.019 0.001 PHE A 557 TYR 0.007 0.001 TYR A 383 ARG 0.001 0.000 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 VAL cc_start: 0.8041 (OUTLIER) cc_final: 0.7798 (t) REVERT: A 119 PHE cc_start: 0.6777 (p90) cc_final: 0.5916 (p90) REVERT: A 150 ILE cc_start: 0.5843 (OUTLIER) cc_final: 0.5584 (mp) REVERT: A 363 GLU cc_start: 0.6354 (tp30) cc_final: 0.6039 (tp30) REVERT: A 418 LYS cc_start: 0.8053 (mppt) cc_final: 0.7841 (mppt) REVERT: A 437 ASP cc_start: 0.5616 (OUTLIER) cc_final: 0.5386 (t70) REVERT: A 642 MET cc_start: 0.7746 (mmm) cc_final: 0.7166 (tmm) outliers start: 21 outliers final: 14 residues processed: 104 average time/residue: 0.8628 time to fit residues: 96.1934 Evaluate side-chains 103 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 695 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 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 = 0.4435 r_free = 0.4435 target = 0.176185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.154967 restraints weight = 8111.283| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 2.74 r_work: 0.4049 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6104 Z= 0.225 Angle : 0.645 9.432 8278 Z= 0.322 Chirality : 0.048 0.395 1004 Planarity : 0.004 0.077 1041 Dihedral : 6.916 55.904 1070 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 3.00 % Allowed : 18.44 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.32 (0.30), residues: 713 helix: -0.42 (0.59), residues: 73 sheet: -4.36 (0.56), residues: 63 loop : -2.41 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 452 HIS 0.004 0.001 HIS A 359 PHE 0.024 0.001 PHE A 557 TYR 0.007 0.001 TYR A 383 ARG 0.001 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7811 (t) REVERT: A 119 PHE cc_start: 0.6793 (p90) cc_final: 0.5940 (p90) REVERT: A 150 ILE cc_start: 0.5850 (OUTLIER) cc_final: 0.5603 (mp) REVERT: A 363 GLU cc_start: 0.6324 (tp30) cc_final: 0.5980 (tp30) REVERT: A 418 LYS cc_start: 0.8054 (mppt) cc_final: 0.7845 (mppt) REVERT: A 437 ASP cc_start: 0.5655 (OUTLIER) cc_final: 0.5424 (t70) REVERT: A 642 MET cc_start: 0.7733 (mmm) cc_final: 0.7078 (tmm) outliers start: 20 outliers final: 14 residues processed: 101 average time/residue: 0.8395 time to fit residues: 90.8143 Evaluate side-chains 100 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 675 TYR Chi-restraints excluded: chain A residue 695 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 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 = 0.4391 r_free = 0.4391 target = 0.172616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.151574 restraints weight = 8149.625| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 2.72 r_work: 0.4013 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 6104 Z= 0.386 Angle : 0.748 9.415 8278 Z= 0.371 Chirality : 0.053 0.407 1004 Planarity : 0.005 0.075 1041 Dihedral : 7.247 55.642 1070 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.57 % Favored : 84.43 % Rotamer: Outliers : 3.00 % Allowed : 18.44 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.30), residues: 713 helix: -0.74 (0.59), residues: 74 sheet: -4.54 (0.54), residues: 63 loop : -2.57 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 296 HIS 0.004 0.001 HIS A 60 PHE 0.040 0.002 PHE A 557 TYR 0.013 0.002 TYR A 675 ARG 0.002 0.000 ARG A 544 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7811 (t) REVERT: A 119 PHE cc_start: 0.6885 (p90) cc_final: 0.6037 (p90) REVERT: A 150 ILE cc_start: 0.5839 (OUTLIER) cc_final: 0.5603 (mp) REVERT: A 363 GLU cc_start: 0.6360 (tp30) cc_final: 0.6010 (tp30) REVERT: A 437 ASP cc_start: 0.5732 (OUTLIER) cc_final: 0.5493 (t70) REVERT: A 642 MET cc_start: 0.7710 (mmm) cc_final: 0.6855 (tmm) outliers start: 20 outliers final: 11 residues processed: 101 average time/residue: 0.8347 time to fit residues: 90.3637 Evaluate side-chains 98 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 675 TYR Chi-restraints excluded: chain A residue 695 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 56 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 58 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.174790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.153715 restraints weight = 8184.958| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.74 r_work: 0.4038 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6104 Z= 0.216 Angle : 0.653 9.434 8278 Z= 0.325 Chirality : 0.048 0.406 1004 Planarity : 0.004 0.072 1041 Dihedral : 6.944 55.948 1070 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 2.40 % Allowed : 19.64 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.30), residues: 713 helix: -0.49 (0.59), residues: 73 sheet: -4.39 (0.56), residues: 63 loop : -2.43 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 546 HIS 0.004 0.001 HIS A 539 PHE 0.020 0.001 PHE A 557 TYR 0.008 0.001 TYR A 383 ARG 0.001 0.000 ARG A 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4522.95 seconds wall clock time: 80 minutes 34.74 seconds (4834.74 seconds total)