Starting phenix.real_space_refine on Sat May 10 10:23:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yhu_39301/05_2025/8yhu_39301.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yhu_39301/05_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_39301/05_2025/8yhu_39301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yhu_39301/05_2025/8yhu_39301.map" model { file = "/net/cci-nas-00/data/ceres_data/8yhu_39301/05_2025/8yhu_39301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yhu_39301/05_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-5687/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: 4.80, per 1000 atoms: 0.80 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: 1.56 Conformation dependent library (CDL) restraints added in 776.2 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: 0.59 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: 1.68 Time building geometry restraints manager: 1.83 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: 0.010 Normalize map: mean=0, sd=1: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.220 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.090 ------------------------------------------------------------------------------- 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 6123 Z= 0.209 Angle : 0.744 11.119 8331 Z= 0.374 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00591 ( 10) link_NAG-ASN : angle 3.21791 ( 30) link_BETA1-4 : bond 0.00302 ( 5) link_BETA1-4 : angle 0.98513 ( 15) hydrogen bonds : bond 0.26987 ( 59) hydrogen bonds : angle 7.25241 ( 141) SS BOND : bond 0.00130 ( 4) SS BOND : angle 1.06445 ( 8) covalent geometry : bond 0.00419 ( 6104) covalent geometry : angle 0.71835 ( 8278) *********************** 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 : 0.671 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: 0.8735 time to fit residues: 94.3215 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 : 0.676 ------------------------------------------------------------------------------- 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 6123 Z= 0.195 Angle : 0.750 10.714 8331 Z= 0.361 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00627 ( 10) link_NAG-ASN : angle 3.11139 ( 30) link_BETA1-4 : bond 0.00456 ( 5) link_BETA1-4 : angle 1.26270 ( 15) hydrogen bonds : bond 0.05496 ( 59) hydrogen bonds : angle 5.62581 ( 141) SS BOND : bond 0.00175 ( 4) SS BOND : angle 0.78447 ( 8) covalent geometry : bond 0.00453 ( 6104) covalent geometry : angle 0.72593 ( 8278) *********************** 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 : 0.650 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: 0.7981 time to fit residues: 87.3444 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 : 0.592 ------------------------------------------------------------------------------- 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 6123 Z= 0.229 Angle : 0.748 10.826 8331 Z= 0.363 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00634 ( 10) link_NAG-ASN : angle 3.22378 ( 30) link_BETA1-4 : bond 0.00556 ( 5) link_BETA1-4 : angle 1.39719 ( 15) hydrogen bonds : bond 0.05473 ( 59) hydrogen bonds : angle 5.38331 ( 141) SS BOND : bond 0.00209 ( 4) SS BOND : angle 0.78628 ( 8) covalent geometry : bond 0.00528 ( 6104) covalent geometry : angle 0.72190 ( 8278) *********************** 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 : 0.686 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: 0.8122 time to fit residues: 88.8379 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 : 0.705 ------------------------------------------------------------------------------- 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 6123 Z= 0.221 Angle : 0.748 10.808 8331 Z= 0.360 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00623 ( 10) link_NAG-ASN : angle 3.20817 ( 30) link_BETA1-4 : bond 0.00528 ( 5) link_BETA1-4 : angle 1.60525 ( 15) hydrogen bonds : bond 0.04993 ( 59) hydrogen bonds : angle 5.21129 ( 141) SS BOND : bond 0.00207 ( 4) SS BOND : angle 0.79630 ( 8) covalent geometry : bond 0.00502 ( 6104) covalent geometry : angle 0.72105 ( 8278) *********************** 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 : 0.669 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: 0.8438 time to fit residues: 93.1694 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 : 0.605 ------------------------------------------------------------------------------- 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: 0.4980 chunk 64 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 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: 0.9980 chunk 47 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4428 r_free = 0.4428 target = 0.175419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.154299 restraints weight = 8157.040| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 2.72 r_work: 0.4044 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6123 Z= 0.165 Angle : 0.698 10.449 8331 Z= 0.338 Chirality : 0.049 0.387 1004 Planarity : 0.004 0.044 1041 Dihedral : 7.669 55.785 1070 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.76 % Favored : 87.24 % Rotamer: Outliers : 3.45 % Allowed : 14.99 % Favored : 81.56 % 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: -3.45 (0.30), residues: 713 helix: -0.53 (0.60), residues: 74 sheet: -4.57 (0.49), residues: 73 loop : -2.43 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 296 HIS 0.003 0.001 HIS A 359 PHE 0.024 0.002 PHE A 557 TYR 0.008 0.001 TYR A 383 ARG 0.002 0.000 ARG A 484 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 10) link_NAG-ASN : angle 3.20804 ( 30) link_BETA1-4 : bond 0.00502 ( 5) link_BETA1-4 : angle 1.69167 ( 15) hydrogen bonds : bond 0.04389 ( 59) hydrogen bonds : angle 5.14165 ( 141) SS BOND : bond 0.00146 ( 4) SS BOND : angle 0.72079 ( 8) covalent geometry : bond 0.00376 ( 6104) covalent geometry : angle 0.66909 ( 8278) *********************** 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 112 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7814 (t) REVERT: A 119 PHE cc_start: 0.6760 (p90) cc_final: 0.5932 (p90) REVERT: A 150 ILE cc_start: 0.5869 (OUTLIER) cc_final: 0.5640 (mp) REVERT: A 642 MET cc_start: 0.7680 (mmm) cc_final: 0.6921 (tmm) outliers start: 23 outliers final: 11 residues processed: 105 average time/residue: 0.7837 time to fit residues: 88.6008 Evaluate side-chains 98 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 675 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 65 optimal weight: 0.0770 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.4443 r_free = 0.4443 target = 0.176868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.155904 restraints weight = 8006.269| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 2.71 r_work: 0.4063 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6123 Z= 0.130 Angle : 0.681 10.660 8331 Z= 0.323 Chirality : 0.048 0.389 1004 Planarity : 0.004 0.041 1041 Dihedral : 7.194 56.071 1070 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 2.85 % Allowed : 17.24 % Favored : 79.91 % 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: -0.53 (0.59), residues: 74 sheet: -4.29 (0.54), residues: 68 loop : -2.37 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 452 HIS 0.003 0.001 HIS A 359 PHE 0.017 0.001 PHE A 557 TYR 0.007 0.001 TYR A 383 ARG 0.001 0.000 ARG A 484 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 10) link_NAG-ASN : angle 3.03705 ( 30) link_BETA1-4 : bond 0.00391 ( 5) link_BETA1-4 : angle 1.64431 ( 15) hydrogen bonds : bond 0.03893 ( 59) hydrogen bonds : angle 5.06753 ( 141) SS BOND : bond 0.00086 ( 4) SS BOND : angle 0.66346 ( 8) covalent geometry : bond 0.00297 ( 6104) covalent geometry : angle 0.65412 ( 8278) *********************** 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 105 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7804 (t) REVERT: A 119 PHE cc_start: 0.6729 (p90) cc_final: 0.5900 (p90) REVERT: A 150 ILE cc_start: 0.5879 (OUTLIER) cc_final: 0.5630 (mp) REVERT: A 363 GLU cc_start: 0.6382 (tp30) cc_final: 0.6078 (tp30) REVERT: A 418 LYS cc_start: 0.8043 (mppt) cc_final: 0.7833 (mppt) REVERT: A 437 ASP cc_start: 0.5598 (OUTLIER) cc_final: 0.5373 (t70) REVERT: A 642 MET cc_start: 0.7572 (mmm) cc_final: 0.7291 (tpp) outliers start: 19 outliers final: 11 residues processed: 101 average time/residue: 0.8262 time to fit residues: 89.5984 Evaluate side-chains 95 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 593 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 0.2980 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4444 r_free = 0.4444 target = 0.176868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.155659 restraints weight = 8125.907| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 2.74 r_work: 0.4062 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6123 Z= 0.131 Angle : 0.666 10.318 8331 Z= 0.320 Chirality : 0.047 0.388 1004 Planarity : 0.004 0.046 1041 Dihedral : 6.970 55.969 1070 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 3.15 % Allowed : 17.69 % Favored : 79.16 % 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: -3.25 (0.30), residues: 713 helix: -0.44 (0.59), residues: 74 sheet: -4.26 (0.54), residues: 68 loop : -2.32 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 296 HIS 0.003 0.001 HIS A 359 PHE 0.019 0.001 PHE A 557 TYR 0.006 0.001 TYR A 383 ARG 0.001 0.000 ARG A 635 Details of bonding type rmsd link_NAG-ASN : bond 0.00558 ( 10) link_NAG-ASN : angle 3.00178 ( 30) link_BETA1-4 : bond 0.00439 ( 5) link_BETA1-4 : angle 1.60138 ( 15) hydrogen bonds : bond 0.03893 ( 59) hydrogen bonds : angle 4.97905 ( 141) SS BOND : bond 0.00095 ( 4) SS BOND : angle 0.62993 ( 8) covalent geometry : bond 0.00300 ( 6104) covalent geometry : angle 0.63879 ( 8278) *********************** 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 106 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 VAL cc_start: 0.8044 (OUTLIER) cc_final: 0.7794 (t) REVERT: A 119 PHE cc_start: 0.6722 (p90) cc_final: 0.5880 (p90) REVERT: A 150 ILE cc_start: 0.5845 (OUTLIER) cc_final: 0.5595 (mp) REVERT: A 363 GLU cc_start: 0.6334 (tp30) cc_final: 0.6022 (tp30) REVERT: A 418 LYS cc_start: 0.8055 (mppt) cc_final: 0.7839 (mppt) REVERT: A 437 ASP cc_start: 0.5597 (OUTLIER) cc_final: 0.5367 (t70) REVERT: A 642 MET cc_start: 0.7583 (mmm) cc_final: 0.7329 (tpp) outliers start: 21 outliers final: 13 residues processed: 102 average time/residue: 0.8203 time to fit residues: 89.5079 Evaluate side-chains 98 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 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 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 695 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 0.0470 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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** A 609 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.176353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.155137 restraints weight = 8056.989| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 2.72 r_work: 0.4052 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6123 Z= 0.158 Angle : 0.686 10.471 8331 Z= 0.330 Chirality : 0.048 0.389 1004 Planarity : 0.004 0.044 1041 Dihedral : 6.945 55.905 1070 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.36 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: -3.29 (0.30), residues: 713 helix: -0.49 (0.59), residues: 74 sheet: -4.27 (0.54), residues: 68 loop : -2.35 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 635 Details of bonding type rmsd link_NAG-ASN : bond 0.00579 ( 10) link_NAG-ASN : angle 3.04723 ( 30) link_BETA1-4 : bond 0.00435 ( 5) link_BETA1-4 : angle 1.55350 ( 15) hydrogen bonds : bond 0.04200 ( 59) hydrogen bonds : angle 4.93863 ( 141) SS BOND : bond 0.00125 ( 4) SS BOND : angle 0.60844 ( 8) covalent geometry : bond 0.00363 ( 6104) covalent geometry : angle 0.65951 ( 8278) *********************** 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 106 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7809 (t) REVERT: A 119 PHE cc_start: 0.6761 (p90) cc_final: 0.5917 (p90) REVERT: A 150 ILE cc_start: 0.5855 (OUTLIER) cc_final: 0.5612 (mp) REVERT: A 363 GLU cc_start: 0.6350 (tp30) cc_final: 0.6031 (tp30) REVERT: A 418 LYS cc_start: 0.8065 (mppt) cc_final: 0.7857 (mppt) REVERT: A 437 ASP cc_start: 0.5651 (OUTLIER) cc_final: 0.5414 (t70) REVERT: A 642 MET cc_start: 0.7556 (mmm) cc_final: 0.7317 (tpp) outliers start: 21 outliers final: 13 residues processed: 103 average time/residue: 0.7741 time to fit residues: 85.9112 Evaluate side-chains 100 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 169 GLN Chi-restraints excluded: chain A residue 297 LEU 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 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: 0.0980 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4432 r_free = 0.4432 target = 0.176036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.154946 restraints weight = 8082.087| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 2.73 r_work: 0.4052 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6123 Z= 0.137 Angle : 0.664 10.329 8331 Z= 0.322 Chirality : 0.047 0.392 1004 Planarity : 0.004 0.042 1041 Dihedral : 6.804 56.006 1070 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 3.00 % Allowed : 18.59 % Favored : 78.41 % 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: -3.23 (0.30), residues: 713 helix: -0.40 (0.59), residues: 74 sheet: -4.23 (0.54), residues: 68 loop : -2.32 (0.26), residues: 571 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 0.002 0.000 ARG A 484 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 10) link_NAG-ASN : angle 2.98222 ( 30) link_BETA1-4 : bond 0.00405 ( 5) link_BETA1-4 : angle 1.47504 ( 15) hydrogen bonds : bond 0.03930 ( 59) hydrogen bonds : angle 4.87785 ( 141) SS BOND : bond 0.00100 ( 4) SS BOND : angle 0.59946 ( 8) covalent geometry : bond 0.00316 ( 6104) covalent geometry : angle 0.63817 ( 8278) *********************** 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 106 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7802 (t) REVERT: A 119 PHE cc_start: 0.6778 (p90) cc_final: 0.5929 (p90) REVERT: A 150 ILE cc_start: 0.5844 (OUTLIER) cc_final: 0.5596 (mp) REVERT: A 363 GLU cc_start: 0.6334 (tp30) cc_final: 0.6006 (tp30) REVERT: A 418 LYS cc_start: 0.8078 (mppt) cc_final: 0.7865 (mppt) REVERT: A 437 ASP cc_start: 0.5626 (OUTLIER) cc_final: 0.5401 (t70) REVERT: A 642 MET cc_start: 0.7496 (mmm) cc_final: 0.7276 (tpp) outliers start: 20 outliers final: 15 residues processed: 101 average time/residue: 0.7953 time to fit residues: 86.4937 Evaluate side-chains 102 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 135 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 297 LEU 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 621 LEU 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: 0.7980 chunk 56 optimal weight: 1.9990 chunk 58 optimal weight: 0.0870 chunk 14 optimal weight: 0.0170 chunk 23 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.4439 r_free = 0.4439 target = 0.176845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.155555 restraints weight = 8120.684| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 2.76 r_work: 0.4053 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6123 Z= 0.130 Angle : 0.660 10.292 8331 Z= 0.318 Chirality : 0.047 0.391 1004 Planarity : 0.004 0.045 1041 Dihedral : 6.690 55.969 1070 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 2.85 % Allowed : 19.19 % 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: -3.22 (0.30), residues: 713 helix: -0.38 (0.60), residues: 74 sheet: -4.17 (0.55), residues: 68 loop : -2.32 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 546 HIS 0.003 0.001 HIS A 319 PHE 0.018 0.001 PHE A 557 TYR 0.007 0.001 TYR A 383 ARG 0.001 0.000 ARG A 73 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 10) link_NAG-ASN : angle 2.95562 ( 30) link_BETA1-4 : bond 0.00372 ( 5) link_BETA1-4 : angle 1.39507 ( 15) hydrogen bonds : bond 0.03904 ( 59) hydrogen bonds : angle 4.78850 ( 141) SS BOND : bond 0.00099 ( 4) SS BOND : angle 0.59876 ( 8) covalent geometry : bond 0.00299 ( 6104) covalent geometry : angle 0.63465 ( 8278) ********************** 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: 19 poor density : 85 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7810 (t) REVERT: A 119 PHE cc_start: 0.6769 (p90) cc_final: 0.5921 (p90) REVERT: A 150 ILE cc_start: 0.5852 (OUTLIER) cc_final: 0.5603 (mp) REVERT: A 363 GLU cc_start: 0.6328 (tp30) cc_final: 0.6001 (tp30) REVERT: A 418 LYS cc_start: 0.8076 (mppt) cc_final: 0.7865 (mppt) REVERT: A 437 ASP cc_start: 0.5632 (OUTLIER) cc_final: 0.5400 (t70) REVERT: A 642 MET cc_start: 0.7478 (mmm) cc_final: 0.7254 (tpp) outliers start: 19 outliers final: 15 residues processed: 101 average time/residue: 0.8191 time to fit residues: 88.4837 Evaluate side-chains 103 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 135 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 297 LEU 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 621 LEU 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: 0.2980 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 44 optimal weight: 0.0000 overall best weight: 0.3984 ------------------------------------------------------------------------------- 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 = 0.4447 r_free = 0.4447 target = 0.177631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.156241 restraints weight = 8178.021| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 2.77 r_work: 0.4060 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6123 Z= 0.113 Angle : 0.636 10.118 8331 Z= 0.307 Chirality : 0.047 0.387 1004 Planarity : 0.004 0.045 1041 Dihedral : 6.528 55.959 1070 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 2.70 % Allowed : 18.89 % Favored : 78.41 % 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: -3.13 (0.30), residues: 713 helix: -0.21 (0.60), residues: 73 sheet: -3.94 (0.56), residues: 70 loop : -2.28 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 452 HIS 0.003 0.001 HIS A 539 PHE 0.014 0.001 PHE A 119 TYR 0.007 0.001 TYR A 383 ARG 0.002 0.000 ARG A 73 Details of bonding type rmsd link_NAG-ASN : bond 0.00557 ( 10) link_NAG-ASN : angle 2.86937 ( 30) link_BETA1-4 : bond 0.00382 ( 5) link_BETA1-4 : angle 1.31557 ( 15) hydrogen bonds : bond 0.03633 ( 59) hydrogen bonds : angle 4.65091 ( 141) SS BOND : bond 0.00068 ( 4) SS BOND : angle 0.61690 ( 8) covalent geometry : bond 0.00258 ( 6104) covalent geometry : angle 0.61084 ( 8278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4662.44 seconds wall clock time: 81 minutes 0.07 seconds (4860.07 seconds total)