Starting phenix.real_space_refine on Tue Jun 10 13:01:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2p_27145/06_2025/8d2p_27145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2p_27145/06_2025/8d2p_27145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d2p_27145/06_2025/8d2p_27145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2p_27145/06_2025/8d2p_27145.map" model { file = "/net/cci-nas-00/data/ceres_data/8d2p_27145/06_2025/8d2p_27145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2p_27145/06_2025/8d2p_27145.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 128 5.49 5 Mg 10 5.21 5 S 20 5.16 5 C 6655 2.51 5 N 2109 2.21 5 O 2514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11436 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8720 Classifications: {'peptide': 1105} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 59, 'TRANS': 1041} Chain breaks: 3 Chain: "B" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2189 Unusual residues: {'GTP': 1} Classifications: {'RNA': 101, 'undetermined': 1} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 46, 'rna3p_pyr': 42} Link IDs: {'rna2p': 13, 'rna3p': 87, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain breaks: 1 Chain: "T" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 481 Classifications: {'DNA': 24} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 7.27, per 1000 atoms: 0.64 Number of scatterers: 11436 At special positions: 0 Unit cell: (94.05, 106.425, 130.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 128 15.00 Mg 10 11.99 O 2514 8.00 N 2109 7.00 C 6655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.3 seconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 49.9% alpha, 8.8% beta 41 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 59 through 92 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 120 through 138 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 180 through 192 Processing helix chain 'A' and resid 221 through 237 removed outlier: 3.569A pdb=" N VAL A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 279 through 293 Processing helix chain 'A' and resid 306 through 319 Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 364 through 377 Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 392 through 405 Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 441 through 456 Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 486 through 508 Processing helix chain 'A' and resid 524 through 552 Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 611 through 618 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 633 through 643 Processing helix chain 'A' and resid 653 through 669 Processing helix chain 'A' and resid 681 through 703 Processing helix chain 'A' and resid 711 through 721 removed outlier: 3.976A pdb=" N THR A 715 " --> pdb=" O ARG A 711 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A 717 " --> pdb=" O GLY A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 742 through 747 removed outlier: 4.009A pdb=" N LEU A 745 " --> pdb=" O THR A 742 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP A 746 " --> pdb=" O LYS A 743 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ARG A 747 " --> pdb=" O ARG A 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 742 through 747' Processing helix chain 'A' and resid 748 through 758 Processing helix chain 'A' and resid 761 through 777 Processing helix chain 'A' and resid 797 through 807 Processing helix chain 'A' and resid 809 through 820 removed outlier: 3.690A pdb=" N ARG A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 860 Processing helix chain 'A' and resid 864 through 876 Processing helix chain 'A' and resid 957 through 963 Processing helix chain 'A' and resid 981 through 986 Processing helix chain 'A' and resid 988 through 997 Processing helix chain 'A' and resid 1025 through 1030 Processing helix chain 'A' and resid 1058 through 1068 Processing helix chain 'A' and resid 1076 through 1086 Processing helix chain 'A' and resid 1093 through 1098 Processing sheet with id=AA1, first strand: chain 'A' and resid 706 through 710 removed outlier: 6.370A pdb=" N ILE A 513 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N PHE A 710 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 515 " --> pdb=" O PHE A 710 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TRP A 13 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N VAL A 514 " --> pdb=" O TRP A 13 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU A 15 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLU A 516 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL A 17 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 24 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 43 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 26 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA A 41 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA A 28 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ILE A 39 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER A 30 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 301 through 304 Processing sheet with id=AA3, first strand: chain 'A' and resid 588 through 591 Processing sheet with id=AA4, first strand: chain 'A' and resid 846 through 849 Processing sheet with id=AA5, first strand: chain 'A' and resid 854 through 855 Processing sheet with id=AA6, first strand: chain 'A' and resid 921 through 924 Processing sheet with id=AA7, first strand: chain 'A' and resid 948 through 956 removed outlier: 3.738A pdb=" N GLY A1004 " --> pdb=" O VAL A 939 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG A 941 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLN A1002 " --> pdb=" O ARG A 941 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1090 through 1091 removed outlier: 6.748A pdb=" N ASN A1050 " --> pdb=" O THR A1041 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU A1011 " --> pdb=" O ILE A1106 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 106 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 6.26 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2585 1.33 - 1.45: 3122 1.45 - 1.57: 5902 1.57 - 1.69: 252 1.69 - 1.81: 28 Bond restraints: 11889 Sorted by residual: bond pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 1.490 1.558 -0.068 3.00e-02 1.11e+03 5.12e+00 bond pdb=" C3' DC T 36 " pdb=" O3' DC T 36 " ideal model delta sigma weight residual 1.422 1.486 -0.064 3.00e-02 1.11e+03 4.58e+00 bond pdb=" C THR A 761 " pdb=" N PRO A 762 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.36e-02 5.41e+03 2.52e+00 bond pdb=" CG LEU A 872 " pdb=" CD1 LEU A 872 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.39e+00 bond pdb=" N1 DC T 21 " pdb=" C2 DC T 21 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.17e+00 ... (remaining 11884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 16260 2.11 - 4.23: 396 4.23 - 6.34: 51 6.34 - 8.46: 15 8.46 - 10.57: 2 Bond angle restraints: 16724 Sorted by residual: angle pdb=" CG ARG A 323 " pdb=" CD ARG A 323 " pdb=" NE ARG A 323 " ideal model delta sigma weight residual 112.00 122.57 -10.57 2.20e+00 2.07e-01 2.31e+01 angle pdb=" C3' U B 62 " pdb=" O3' U B 62 " pdb=" P C B 63 " ideal model delta sigma weight residual 120.20 125.97 -5.77 1.50e+00 4.44e-01 1.48e+01 angle pdb=" C4' U B 62 " pdb=" C3' U B 62 " pdb=" O3' U B 62 " ideal model delta sigma weight residual 113.00 118.66 -5.66 1.50e+00 4.44e-01 1.42e+01 angle pdb=" C LEU A 722 " pdb=" N ASP A 723 " pdb=" CA ASP A 723 " ideal model delta sigma weight residual 121.54 128.55 -7.01 1.91e+00 2.74e-01 1.35e+01 angle pdb=" C LEU A 416 " pdb=" N LEU A 417 " pdb=" CA LEU A 417 " ideal model delta sigma weight residual 121.54 128.53 -6.99 1.91e+00 2.74e-01 1.34e+01 ... (remaining 16719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.86: 6777 29.86 - 59.71: 374 59.71 - 89.57: 120 89.57 - 119.42: 3 119.42 - 149.28: 3 Dihedral angle restraints: 7277 sinusoidal: 4081 harmonic: 3196 Sorted by residual: dihedral pdb=" C5' GTP B 1 " pdb=" O5' GTP B 1 " pdb=" PA GTP B 1 " pdb=" O3A GTP B 1 " ideal model delta sinusoidal sigma weight residual 69.27 162.88 -93.61 1 2.00e+01 2.50e-03 2.55e+01 dihedral pdb=" C8 GTP B 1 " pdb=" C1' GTP B 1 " pdb=" N9 GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sinusoidal sigma weight residual 104.59 13.60 90.99 1 2.00e+01 2.50e-03 2.44e+01 dihedral pdb=" CA ILE A 592 " pdb=" C ILE A 592 " pdb=" N VAL A 593 " pdb=" CA VAL A 593 " ideal model delta harmonic sigma weight residual 180.00 157.55 22.45 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 7274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1587 0.058 - 0.116: 293 0.116 - 0.175: 39 0.175 - 0.233: 8 0.233 - 0.291: 3 Chirality restraints: 1930 Sorted by residual: chirality pdb=" CG LEU A 84 " pdb=" CB LEU A 84 " pdb=" CD1 LEU A 84 " pdb=" CD2 LEU A 84 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CG LEU A1075 " pdb=" CB LEU A1075 " pdb=" CD1 LEU A1075 " pdb=" CD2 LEU A1075 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C1' G B 30 " pdb=" O4' G B 30 " pdb=" C2' G B 30 " pdb=" N9 G B 30 " both_signs ideal model delta sigma weight residual False 2.46 2.21 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1927 not shown) Planarity restraints: 1714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 363 " 0.024 2.00e-02 2.50e+03 3.23e-02 1.82e+01 pdb=" CG PHE A 363 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE A 363 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE A 363 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 363 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 363 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 363 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 800 " 0.009 2.00e-02 2.50e+03 1.96e-02 7.68e+00 pdb=" CG TYR A 800 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 800 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 800 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR A 800 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 800 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 800 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 800 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 187 " -0.001 2.00e-02 2.50e+03 1.95e-02 7.60e+00 pdb=" CG TYR A 187 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 187 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A 187 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A 187 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 187 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 187 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 187 " -0.014 2.00e-02 2.50e+03 ... (remaining 1711 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 134 2.59 - 3.17: 8583 3.17 - 3.75: 20848 3.75 - 4.32: 27910 4.32 - 4.90: 42434 Nonbonded interactions: 99909 Sorted by model distance: nonbonded pdb="MG MG A1201 " pdb=" O HOH A1304 " model vdw 2.018 2.170 nonbonded pdb=" OD1 ASP A 590 " pdb="MG MG A1201 " model vdw 2.021 2.170 nonbonded pdb=" OP2 DC T 14 " pdb="MG MG A1201 " model vdw 2.036 2.170 nonbonded pdb=" OD1 ASN A 614 " pdb="MG MG A1201 " model vdw 2.045 2.170 nonbonded pdb="MG MG B 202 " pdb=" O HOH B 312 " model vdw 2.085 2.170 ... (remaining 99904 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.850 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 33.820 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.005 0.068 11891 Z= 0.215 Angle : 0.806 10.570 16724 Z= 0.423 Chirality : 0.047 0.291 1930 Planarity : 0.008 0.108 1714 Dihedral : 18.654 149.279 5203 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: -1.23 (0.22), residues: 1097 helix: -0.68 (0.19), residues: 528 sheet: -0.70 (0.48), residues: 89 loop : -0.81 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 161 HIS 0.005 0.002 HIS A1037 PHE 0.069 0.003 PHE A 363 TYR 0.047 0.004 TYR A 800 ARG 0.014 0.001 ARG A 544 Details of bonding type rmsd hydrogen bonds : bond 0.06535 ( 522) hydrogen bonds : angle 5.30919 ( 1409) covalent geometry : bond 0.00453 (11889) covalent geometry : angle 0.80643 (16724) Misc. bond : bond 0.00168 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.053 Fit side-chains REVERT: A 155 PRO cc_start: 0.7570 (Cg_endo) cc_final: 0.7300 (Cg_exo) REVERT: A 572 ASP cc_start: 0.7804 (t0) cc_final: 0.7578 (t0) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 1.6949 time to fit residues: 205.6028 Evaluate side-chains 84 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.165732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.134445 restraints weight = 11752.238| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.02 r_work: 0.3192 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 11891 Z= 0.264 Angle : 0.655 6.142 16724 Z= 0.339 Chirality : 0.043 0.249 1930 Planarity : 0.007 0.068 1714 Dihedral : 19.486 151.197 3114 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.62 % Allowed : 7.65 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: -0.17 (0.24), residues: 1097 helix: 0.51 (0.21), residues: 536 sheet: -0.85 (0.47), residues: 91 loop : -0.56 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 161 HIS 0.009 0.002 HIS A1100 PHE 0.027 0.003 PHE A 282 TYR 0.016 0.003 TYR A 868 ARG 0.008 0.001 ARG A 659 Details of bonding type rmsd hydrogen bonds : bond 0.05799 ( 522) hydrogen bonds : angle 4.58682 ( 1409) covalent geometry : bond 0.00570 (11889) covalent geometry : angle 0.65506 (16724) Misc. bond : bond 0.00159 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 155 PRO cc_start: 0.7534 (Cg_endo) cc_final: 0.7277 (Cg_exo) REVERT: A 261 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7193 (pm20) REVERT: A 470 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7321 (p0) REVERT: A 572 ASP cc_start: 0.8165 (t0) cc_final: 0.7708 (t0) REVERT: A 597 ASP cc_start: 0.8149 (m-30) cc_final: 0.7902 (m-30) REVERT: A 1118 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7589 (mtm-85) outliers start: 24 outliers final: 9 residues processed: 112 average time/residue: 1.9026 time to fit residues: 226.8085 Evaluate side-chains 99 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 41 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.169697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.146066 restraints weight = 11984.220| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.12 r_work: 0.3171 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11891 Z= 0.128 Angle : 0.523 6.341 16724 Z= 0.272 Chirality : 0.036 0.255 1930 Planarity : 0.005 0.071 1714 Dihedral : 19.344 151.083 3114 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.53 % Allowed : 9.62 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.43 (0.24), residues: 1097 helix: 1.17 (0.22), residues: 536 sheet: -0.97 (0.47), residues: 89 loop : -0.40 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 387 HIS 0.003 0.001 HIS A1100 PHE 0.013 0.001 PHE A 282 TYR 0.013 0.002 TYR A 868 ARG 0.007 0.000 ARG A 775 Details of bonding type rmsd hydrogen bonds : bond 0.04787 ( 522) hydrogen bonds : angle 4.12120 ( 1409) covalent geometry : bond 0.00265 (11889) covalent geometry : angle 0.52340 (16724) Misc. bond : bond 0.00179 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.395 Fit side-chains REVERT: A 155 PRO cc_start: 0.7346 (Cg_endo) cc_final: 0.7088 (Cg_exo) REVERT: A 261 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7151 (pm20) REVERT: A 398 ASP cc_start: 0.6798 (OUTLIER) cc_final: 0.6107 (m-30) REVERT: A 470 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7266 (p0) REVERT: A 572 ASP cc_start: 0.8128 (t0) cc_final: 0.7610 (t0) REVERT: A 597 ASP cc_start: 0.8108 (m-30) cc_final: 0.7883 (m-30) REVERT: A 659 ARG cc_start: 0.7916 (ttm110) cc_final: 0.7624 (ptp-110) outliers start: 14 outliers final: 4 residues processed: 115 average time/residue: 2.4183 time to fit residues: 296.2872 Evaluate side-chains 107 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 815 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 16 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.166941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.135415 restraints weight = 11841.467| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.55 r_work: 0.3142 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11891 Z= 0.155 Angle : 0.540 6.182 16724 Z= 0.280 Chirality : 0.037 0.249 1930 Planarity : 0.005 0.071 1714 Dihedral : 19.286 150.668 3114 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.08 % Allowed : 10.82 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.60 (0.25), residues: 1097 helix: 1.37 (0.22), residues: 534 sheet: -1.00 (0.48), residues: 89 loop : -0.36 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 387 HIS 0.004 0.001 HIS A1100 PHE 0.019 0.002 PHE A 282 TYR 0.012 0.002 TYR A 651 ARG 0.005 0.000 ARG A 719 Details of bonding type rmsd hydrogen bonds : bond 0.04882 ( 522) hydrogen bonds : angle 4.11059 ( 1409) covalent geometry : bond 0.00331 (11889) covalent geometry : angle 0.54003 (16724) Misc. bond : bond 0.00153 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.068 Fit side-chains REVERT: A 155 PRO cc_start: 0.7355 (Cg_endo) cc_final: 0.7084 (Cg_exo) REVERT: A 174 VAL cc_start: 0.7921 (p) cc_final: 0.7538 (m) REVERT: A 261 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7111 (pm20) REVERT: A 398 ASP cc_start: 0.6767 (OUTLIER) cc_final: 0.6055 (m-30) REVERT: A 470 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7263 (p0) REVERT: A 572 ASP cc_start: 0.8113 (t0) cc_final: 0.7597 (t0) REVERT: A 597 ASP cc_start: 0.8139 (m-30) cc_final: 0.7905 (m-30) REVERT: A 717 GLU cc_start: 0.6599 (tt0) cc_final: 0.6066 (mt-10) outliers start: 19 outliers final: 7 residues processed: 110 average time/residue: 1.7527 time to fit residues: 205.1743 Evaluate side-chains 106 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1064 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 99 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 50 optimal weight: 0.0870 chunk 38 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 750 HIS ** 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 = 0.3850 r_free = 0.3850 target = 0.166861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.131438 restraints weight = 11853.787| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.20 r_work: 0.3165 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11891 Z= 0.170 Angle : 0.550 6.100 16724 Z= 0.286 Chirality : 0.038 0.247 1930 Planarity : 0.005 0.072 1714 Dihedral : 19.280 150.394 3114 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.51 % Allowed : 11.26 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.65 (0.25), residues: 1097 helix: 1.43 (0.22), residues: 534 sheet: -1.06 (0.48), residues: 89 loop : -0.34 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 387 HIS 0.005 0.001 HIS A1100 PHE 0.020 0.002 PHE A 282 TYR 0.012 0.002 TYR A 651 ARG 0.006 0.000 ARG A 659 Details of bonding type rmsd hydrogen bonds : bond 0.04957 ( 522) hydrogen bonds : angle 4.10997 ( 1409) covalent geometry : bond 0.00364 (11889) covalent geometry : angle 0.55037 (16724) Misc. bond : bond 0.00146 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 1.629 Fit side-chains revert: symmetry clash REVERT: A 155 PRO cc_start: 0.7330 (Cg_endo) cc_final: 0.7052 (Cg_exo) REVERT: A 174 VAL cc_start: 0.7950 (p) cc_final: 0.7560 (m) REVERT: A 261 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7253 (pm20) REVERT: A 398 ASP cc_start: 0.6877 (OUTLIER) cc_final: 0.6201 (m-30) REVERT: A 527 ARG cc_start: 0.6512 (tpp80) cc_final: 0.5863 (ttt90) REVERT: A 572 ASP cc_start: 0.8251 (t0) cc_final: 0.7754 (t0) REVERT: A 717 GLU cc_start: 0.6727 (tt0) cc_final: 0.6316 (mt-10) REVERT: A 801 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6740 (mtp180) REVERT: A 880 ARG cc_start: 0.6723 (ptt180) cc_final: 0.5923 (ptt90) outliers start: 23 outliers final: 10 residues processed: 106 average time/residue: 2.1914 time to fit residues: 247.7749 Evaluate side-chains 108 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 801 ARG Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1099 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 8 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 750 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.164997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.143349 restraints weight = 11984.205| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.05 r_work: 0.3117 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11891 Z= 0.260 Angle : 0.634 6.567 16724 Z= 0.328 Chirality : 0.042 0.250 1930 Planarity : 0.006 0.072 1714 Dihedral : 19.385 150.324 3114 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.73 % Allowed : 11.58 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.35 (0.25), residues: 1097 helix: 1.05 (0.22), residues: 543 sheet: -1.06 (0.48), residues: 91 loop : -0.38 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 387 HIS 0.005 0.001 HIS A1100 PHE 0.024 0.003 PHE A 282 TYR 0.015 0.003 TYR A 800 ARG 0.006 0.001 ARG A 137 Details of bonding type rmsd hydrogen bonds : bond 0.05535 ( 522) hydrogen bonds : angle 4.38631 ( 1409) covalent geometry : bond 0.00564 (11889) covalent geometry : angle 0.63395 (16724) Misc. bond : bond 0.00137 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 155 PRO cc_start: 0.7467 (Cg_endo) cc_final: 0.7199 (Cg_exo) REVERT: A 261 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7109 (pm20) REVERT: A 398 ASP cc_start: 0.6780 (OUTLIER) cc_final: 0.6083 (m-30) REVERT: A 572 ASP cc_start: 0.8172 (t0) cc_final: 0.7660 (t0) REVERT: A 717 GLU cc_start: 0.6719 (tt0) cc_final: 0.6124 (mt-10) REVERT: A 801 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6675 (mtp180) REVERT: A 880 ARG cc_start: 0.6671 (ptt180) cc_final: 0.5949 (ptt90) REVERT: A 1118 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7429 (mtm-85) outliers start: 25 outliers final: 10 residues processed: 111 average time/residue: 1.7814 time to fit residues: 209.8900 Evaluate side-chains 108 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 801 ARG Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1099 CYS Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 72 optimal weight: 0.1980 chunk 57 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1100 HIS ** 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 = 0.3868 r_free = 0.3868 target = 0.168629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.143640 restraints weight = 12078.883| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.21 r_work: 0.3150 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11891 Z= 0.132 Angle : 0.523 6.721 16724 Z= 0.272 Chirality : 0.037 0.254 1930 Planarity : 0.005 0.072 1714 Dihedral : 19.262 150.691 3114 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.42 % Allowed : 13.22 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.67 (0.25), residues: 1097 helix: 1.38 (0.22), residues: 543 sheet: -1.10 (0.48), residues: 89 loop : -0.27 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 387 HIS 0.003 0.001 HIS A 134 PHE 0.014 0.001 PHE A 282 TYR 0.013 0.002 TYR A 651 ARG 0.006 0.000 ARG A1088 Details of bonding type rmsd hydrogen bonds : bond 0.04753 ( 522) hydrogen bonds : angle 4.06692 ( 1409) covalent geometry : bond 0.00280 (11889) covalent geometry : angle 0.52337 (16724) Misc. bond : bond 0.00164 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 1.092 Fit side-chains REVERT: A 155 PRO cc_start: 0.7232 (Cg_endo) cc_final: 0.6957 (Cg_exo) REVERT: A 174 VAL cc_start: 0.7935 (p) cc_final: 0.7572 (m) REVERT: A 261 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7098 (pm20) REVERT: A 398 ASP cc_start: 0.6733 (OUTLIER) cc_final: 0.6003 (m-30) REVERT: A 474 ARG cc_start: 0.8152 (mmt180) cc_final: 0.7842 (mmt180) REVERT: A 527 ARG cc_start: 0.6419 (tpp80) cc_final: 0.5786 (ttt90) REVERT: A 572 ASP cc_start: 0.8179 (t0) cc_final: 0.7659 (t0) REVERT: A 717 GLU cc_start: 0.6617 (tt0) cc_final: 0.6281 (mt-10) REVERT: A 719 ARG cc_start: 0.6937 (ttp-110) cc_final: 0.6591 (mtp85) REVERT: A 880 ARG cc_start: 0.6671 (ptt180) cc_final: 0.5909 (ptt90) outliers start: 13 outliers final: 9 residues processed: 108 average time/residue: 1.8150 time to fit residues: 207.8718 Evaluate side-chains 107 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1064 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 86 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** A1100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.167976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.144374 restraints weight = 12036.486| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.10 r_work: 0.3143 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11891 Z= 0.150 Angle : 0.532 6.560 16724 Z= 0.276 Chirality : 0.037 0.249 1930 Planarity : 0.005 0.072 1714 Dihedral : 19.226 150.238 3114 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.64 % Allowed : 13.77 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.71 (0.25), residues: 1097 helix: 1.41 (0.22), residues: 543 sheet: -1.06 (0.49), residues: 89 loop : -0.25 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 387 HIS 0.003 0.001 HIS A1100 PHE 0.017 0.002 PHE A 282 TYR 0.013 0.002 TYR A 651 ARG 0.006 0.000 ARG A1088 Details of bonding type rmsd hydrogen bonds : bond 0.04822 ( 522) hydrogen bonds : angle 4.04875 ( 1409) covalent geometry : bond 0.00320 (11889) covalent geometry : angle 0.53221 (16724) Misc. bond : bond 0.00144 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.981 Fit side-chains REVERT: A 174 VAL cc_start: 0.8009 (p) cc_final: 0.7660 (m) REVERT: A 261 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7079 (pm20) REVERT: A 398 ASP cc_start: 0.6743 (OUTLIER) cc_final: 0.6006 (m-30) REVERT: A 527 ARG cc_start: 0.6461 (tpp80) cc_final: 0.5805 (ttt90) REVERT: A 550 ARG cc_start: 0.7111 (mpt-90) cc_final: 0.6830 (mpt-90) REVERT: A 572 ASP cc_start: 0.8177 (t0) cc_final: 0.7652 (t0) REVERT: A 717 GLU cc_start: 0.6581 (tt0) cc_final: 0.6186 (mt-10) REVERT: A 719 ARG cc_start: 0.6962 (ttp-110) cc_final: 0.6581 (mtp85) REVERT: A 880 ARG cc_start: 0.6669 (ptt180) cc_final: 0.5902 (ptt90) outliers start: 15 outliers final: 8 residues processed: 107 average time/residue: 1.9117 time to fit residues: 216.1730 Evaluate side-chains 108 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1064 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 73 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1100 HIS ** 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 = 0.3842 r_free = 0.3842 target = 0.166079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.143934 restraints weight = 11932.098| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.02 r_work: 0.3134 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11891 Z= 0.196 Angle : 0.573 6.621 16724 Z= 0.297 Chirality : 0.039 0.247 1930 Planarity : 0.005 0.072 1714 Dihedral : 19.276 150.050 3114 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.42 % Allowed : 13.88 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.60 (0.25), residues: 1097 helix: 1.27 (0.22), residues: 543 sheet: -0.97 (0.49), residues: 91 loop : -0.26 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 387 HIS 0.004 0.001 HIS A 47 PHE 0.021 0.002 PHE A 282 TYR 0.014 0.002 TYR A 800 ARG 0.006 0.001 ARG A1088 Details of bonding type rmsd hydrogen bonds : bond 0.05105 ( 522) hydrogen bonds : angle 4.18750 ( 1409) covalent geometry : bond 0.00422 (11889) covalent geometry : angle 0.57271 (16724) Misc. bond : bond 0.00142 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 1.041 Fit side-chains REVERT: A 174 VAL cc_start: 0.7998 (p) cc_final: 0.7635 (m) REVERT: A 261 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7092 (pm20) REVERT: A 398 ASP cc_start: 0.6763 (OUTLIER) cc_final: 0.6029 (m-30) REVERT: A 572 ASP cc_start: 0.8159 (t0) cc_final: 0.7641 (t0) REVERT: A 717 GLU cc_start: 0.6638 (tt0) cc_final: 0.6110 (mt-10) REVERT: A 719 ARG cc_start: 0.6999 (ttp-110) cc_final: 0.6629 (mtp85) REVERT: A 880 ARG cc_start: 0.6678 (ptt180) cc_final: 0.5889 (ptt90) REVERT: A 996 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.6092 (mm-30) outliers start: 13 outliers final: 8 residues processed: 102 average time/residue: 1.8666 time to fit residues: 201.9860 Evaluate side-chains 102 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 996 GLU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1064 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 104 optimal weight: 0.0470 chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 0.0040 chunk 59 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.6094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1100 HIS A1120 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.170768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.148833 restraints weight = 11926.087| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.03 r_work: 0.3216 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11891 Z= 0.107 Angle : 0.500 6.944 16724 Z= 0.260 Chirality : 0.036 0.255 1930 Planarity : 0.004 0.072 1714 Dihedral : 19.150 150.492 3114 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.98 % Allowed : 14.21 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.91 (0.25), residues: 1097 helix: 1.57 (0.22), residues: 543 sheet: -0.99 (0.50), residues: 89 loop : -0.14 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 387 HIS 0.002 0.001 HIS A 134 PHE 0.010 0.001 PHE A 282 TYR 0.013 0.002 TYR A 651 ARG 0.007 0.000 ARG A1088 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 522) hydrogen bonds : angle 3.90647 ( 1409) covalent geometry : bond 0.00223 (11889) covalent geometry : angle 0.49957 (16724) Misc. bond : bond 0.00156 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 174 VAL cc_start: 0.7994 (p) cc_final: 0.7645 (m) REVERT: A 398 ASP cc_start: 0.6689 (OUTLIER) cc_final: 0.5950 (m-30) REVERT: A 527 ARG cc_start: 0.6347 (tpp80) cc_final: 0.5719 (ttt90) REVERT: A 550 ARG cc_start: 0.7071 (mpt-90) cc_final: 0.6820 (mpt-90) REVERT: A 572 ASP cc_start: 0.8109 (t0) cc_final: 0.7590 (t0) REVERT: A 649 ASN cc_start: 0.6487 (p0) cc_final: 0.6282 (p0) REVERT: A 717 GLU cc_start: 0.6469 (tt0) cc_final: 0.6162 (mt-10) REVERT: A 719 ARG cc_start: 0.6963 (ttp-110) cc_final: 0.6678 (mtp85) REVERT: A 880 ARG cc_start: 0.6674 (ptt180) cc_final: 0.5911 (ptt90) outliers start: 9 outliers final: 4 residues processed: 111 average time/residue: 1.8185 time to fit residues: 214.3748 Evaluate side-chains 104 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1020 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 81 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 31 optimal weight: 0.0070 chunk 118 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.164599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.142577 restraints weight = 11775.898| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.05 r_work: 0.3110 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11891 Z= 0.271 Angle : 0.645 8.063 16724 Z= 0.334 Chirality : 0.043 0.246 1930 Planarity : 0.006 0.073 1714 Dihedral : 19.338 149.705 3114 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.20 % Allowed : 14.32 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.49 (0.25), residues: 1097 helix: 1.14 (0.22), residues: 542 sheet: -1.02 (0.48), residues: 91 loop : -0.25 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 387 HIS 0.005 0.001 HIS A 603 PHE 0.024 0.003 PHE A 282 TYR 0.027 0.003 TYR A 800 ARG 0.006 0.001 ARG A 137 Details of bonding type rmsd hydrogen bonds : bond 0.05553 ( 522) hydrogen bonds : angle 4.36612 ( 1409) covalent geometry : bond 0.00590 (11889) covalent geometry : angle 0.64549 (16724) Misc. bond : bond 0.00148 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7652.80 seconds wall clock time: 133 minutes 23.54 seconds (8003.54 seconds total)