Starting phenix.real_space_refine on Fri Aug 22 22:38:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h8b_34541/08_2025/8h8b_34541.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h8b_34541/08_2025/8h8b_34541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h8b_34541/08_2025/8h8b_34541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h8b_34541/08_2025/8h8b_34541.map" model { file = "/net/cci-nas-00/data/ceres_data/8h8b_34541/08_2025/8h8b_34541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h8b_34541/08_2025/8h8b_34541.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 13 5.16 5 C 5251 2.51 5 N 1439 2.21 5 O 1641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8344 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8344 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 24, 'TRANS': 1002} Time building chain proxies: 1.46, per 1000 atoms: 0.17 Number of scatterers: 8344 At special positions: 0 Unit cell: (76.56, 89.61, 119.19, 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 13 16.00 O 1641 8.00 N 1439 7.00 C 5251 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=0, symmetry=0 Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 291.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1884 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 17 sheets defined 2.8% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.590A pdb=" N SER A 383 " --> pdb=" O GLU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1112 Processing helix chain 'A' and resid 1139 through 1144 Processing helix chain 'A' and resid 1154 through 1165 Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 170 removed outlier: 6.677A pdb=" N TRP A 177 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 207 removed outlier: 4.363A pdb=" N SER A 216 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 251 removed outlier: 5.891A pdb=" N CYS A 247 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N THR A 258 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N PHE A 249 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE A 256 " --> pdb=" O PHE A 249 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN A 251 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.503A pdb=" N ARG A 290 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 302 removed outlier: 7.072A pdb=" N VAL A 300 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 305 " --> pdb=" O HIS A 302 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 334 through 335 removed outlier: 3.665A pdb=" N ILE A 334 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 343 " --> pdb=" O ILE A 334 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 356 Processing sheet with id=AA8, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.554A pdb=" N GLU A 376 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 400 through 402 removed outlier: 5.513A pdb=" N LEU A 428 " --> pdb=" O TRP A 440 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLU A 449 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE A 470 " --> pdb=" O TYR A 482 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN A 481 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 491 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LYS A 502 " --> pdb=" O ASP A 514 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASP A 514 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 544 through 547 removed outlier: 6.464A pdb=" N ARG A 544 " --> pdb=" O HIS A 556 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS A 556 " --> pdb=" O ARG A 544 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP A 546 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL A 554 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN A 574 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N THR A 595 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ALA A 621 " --> pdb=" O TYR A 632 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR A 662 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 696 through 697 removed outlier: 6.916A pdb=" N LYS A 696 " --> pdb=" O ILE A 704 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 716 through 717 removed outlier: 4.579A pdb=" N GLN A 724 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 726 " --> pdb=" O ASN A 737 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 758 through 763 removed outlier: 7.257A pdb=" N GLN A 758 " --> pdb=" O ARG A 770 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ARG A 770 " --> pdb=" O GLN A 758 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN A 760 " --> pdb=" O THR A 768 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 762 " --> pdb=" O HIS A 766 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N HIS A 766 " --> pdb=" O SER A 762 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 799 through 803 removed outlier: 6.049A pdb=" N ASP A 803 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 808 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 11.855A pdb=" N ARG A 807 " --> pdb=" O TYR A 825 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N TYR A 825 " --> pdb=" O ARG A 807 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N SER A 809 " --> pdb=" O PHE A 823 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 823 " --> pdb=" O SER A 809 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N SER A 832 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU A 853 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL A 852 " --> pdb=" O TYR A 863 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N SER A 872 " --> pdb=" O TYR A 884 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 880 " --> pdb=" O ASP A 876 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 918 through 919 removed outlier: 6.526A pdb=" N LYS A 918 " --> pdb=" O GLU A 925 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLU A 925 " --> pdb=" O TYR A 932 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL A 961 " --> pdb=" O TYR A 972 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N HIS A 971 " --> pdb=" O LYS A 983 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS A 983 " --> pdb=" O HIS A 971 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLU A 973 " --> pdb=" O THR A 981 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N THR A 981 " --> pdb=" O PHE A 992 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU A 991 " --> pdb=" O GLU A1002 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU A1002 " --> pdb=" O GLU A 991 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 993 " --> pdb=" O LEU A1000 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 998 " --> pdb=" O GLU A 995 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A1009 " --> pdb=" O GLU A1002 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A1042 " --> pdb=" O GLU A1033 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLU A1041 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP A1045 " --> pdb=" O ILE A1050 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A1050 " --> pdb=" O ASP A1045 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A1066 " --> pdb=" O SER A1053 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N SER A1055 " --> pdb=" O ILE A1064 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE A1064 " --> pdb=" O SER A1055 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1013 through 1014 removed outlier: 6.205A pdb=" N ILE A1019 " --> pdb=" O GLN A1014 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1079 through 1081 removed outlier: 3.597A pdb=" N ARG A1100 " --> pdb=" O ASP A1095 " (cutoff:3.500A) 219 hydrogen bonds defined for protein. 582 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: 1.77 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2805 1.34 - 1.46: 2083 1.46 - 1.58: 3641 1.58 - 1.69: 0 1.69 - 1.81: 17 Bond restraints: 8546 Sorted by residual: bond pdb=" CA GLU A 271 " pdb=" C GLU A 271 " ideal model delta sigma weight residual 1.519 1.529 -0.009 1.01e-02 9.80e+03 8.60e-01 bond pdb=" CA ILE A1019 " pdb=" CB ILE A1019 " ideal model delta sigma weight residual 1.537 1.525 0.012 1.29e-02 6.01e+03 8.25e-01 bond pdb=" N THR A 332 " pdb=" CA THR A 332 " ideal model delta sigma weight residual 1.460 1.472 -0.012 1.42e-02 4.96e+03 6.85e-01 bond pdb=" N TYR A 242 " pdb=" CA TYR A 242 " ideal model delta sigma weight residual 1.460 1.471 -0.011 1.39e-02 5.18e+03 6.13e-01 bond pdb=" CA VAL A 735 " pdb=" C VAL A 735 " ideal model delta sigma weight residual 1.524 1.531 -0.007 1.01e-02 9.80e+03 5.14e-01 ... (remaining 8541 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 11450 1.63 - 3.26: 100 3.26 - 4.88: 16 4.88 - 6.51: 3 6.51 - 8.14: 1 Bond angle restraints: 11570 Sorted by residual: angle pdb=" N CYS A 147 " pdb=" CA CYS A 147 " pdb=" C CYS A 147 " ideal model delta sigma weight residual 108.24 112.24 -4.00 1.32e+00 5.74e-01 9.20e+00 angle pdb=" C HIS A 302 " pdb=" N ASN A 303 " pdb=" CA ASN A 303 " ideal model delta sigma weight residual 121.54 127.26 -5.72 1.91e+00 2.74e-01 8.98e+00 angle pdb=" N SER A 216 " pdb=" CA SER A 216 " pdb=" C SER A 216 " ideal model delta sigma weight residual 108.32 112.95 -4.63 1.64e+00 3.72e-01 7.98e+00 angle pdb=" N ASP A 397 " pdb=" CA ASP A 397 " pdb=" C ASP A 397 " ideal model delta sigma weight residual 107.93 111.54 -3.61 1.65e+00 3.67e-01 4.80e+00 angle pdb=" CA VAL A 319 " pdb=" C VAL A 319 " pdb=" N GLU A 320 " ideal model delta sigma weight residual 116.60 119.55 -2.95 1.45e+00 4.76e-01 4.14e+00 ... (remaining 11565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4587 17.86 - 35.71: 329 35.71 - 53.57: 58 53.57 - 71.43: 18 71.43 - 89.29: 6 Dihedral angle restraints: 4998 sinusoidal: 2018 harmonic: 2980 Sorted by residual: dihedral pdb=" CA LYS A 304 " pdb=" C LYS A 304 " pdb=" N ARG A 305 " pdb=" CA ARG A 305 " ideal model delta harmonic sigma weight residual -180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CB GLU A 429 " pdb=" CG GLU A 429 " pdb=" CD GLU A 429 " pdb=" OE1 GLU A 429 " ideal model delta sinusoidal sigma weight residual 0.00 -89.29 89.29 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA ASN A 303 " pdb=" C ASN A 303 " pdb=" N LYS A 304 " pdb=" CA LYS A 304 " ideal model delta harmonic sigma weight residual 180.00 164.26 15.74 0 5.00e+00 4.00e-02 9.91e+00 ... (remaining 4995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 705 0.027 - 0.054: 322 0.054 - 0.081: 61 0.081 - 0.108: 68 0.108 - 0.135: 30 Chirality restraints: 1186 Sorted by residual: chirality pdb=" CA THR A 332 " pdb=" N THR A 332 " pdb=" C THR A 332 " pdb=" CB THR A 332 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA ILE A 726 " pdb=" N ILE A 726 " pdb=" C ILE A 726 " pdb=" CB ILE A 726 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA ILE A 597 " pdb=" N ILE A 597 " pdb=" C ILE A 597 " pdb=" CB ILE A 597 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 1183 not shown) Planarity restraints: 1528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 251 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.14e+00 pdb=" N PRO A 252 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 252 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 252 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 453 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 454 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 454 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 454 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A1014 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO A1015 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A1015 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A1015 " 0.016 5.00e-02 4.00e+02 ... (remaining 1525 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1165 2.76 - 3.30: 7163 3.30 - 3.83: 12974 3.83 - 4.37: 15555 4.37 - 4.90: 27797 Nonbonded interactions: 64654 Sorted by model distance: nonbonded pdb=" O SER A 587 " pdb=" OG1 THR A 595 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR A 742 " pdb=" O GLY A 745 " model vdw 2.246 3.040 nonbonded pdb=" O ILE A 871 " pdb=" OH TYR A 886 " model vdw 2.265 3.040 nonbonded pdb=" O THR A 796 " pdb=" OG SER A 814 " model vdw 2.287 3.040 nonbonded pdb=" O GLY A 938 " pdb=" OH TYR A1116 " model vdw 2.317 3.040 ... (remaining 64649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.010 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.250 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 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 : 0.001 0.016 8546 Z= 0.092 Angle : 0.457 8.138 11570 Z= 0.276 Chirality : 0.040 0.135 1186 Planarity : 0.002 0.037 1528 Dihedral : 12.997 89.286 3114 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.67 % Allowed : 6.86 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.99 (0.23), residues: 1025 helix: -1.91 (1.51), residues: 12 sheet: -0.79 (0.37), residues: 188 loop : -2.52 (0.18), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 979 TYR 0.009 0.001 TYR A 242 PHE 0.006 0.000 PHE A 267 TRP 0.003 0.000 TRP A 438 HIS 0.004 0.000 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00150 ( 8546) covalent geometry : angle 0.45656 (11570) hydrogen bonds : bond 0.15430 ( 219) hydrogen bonds : angle 6.30170 ( 582) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.234 Fit side-chains REVERT: A 226 GLU cc_start: 0.5483 (pt0) cc_final: 0.5206 (pt0) REVERT: A 228 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7265 (mm-30) REVERT: A 403 GLU cc_start: 0.6716 (tp30) cc_final: 0.6347 (mm-30) REVERT: A 918 LYS cc_start: 0.7893 (tttt) cc_final: 0.7538 (tttp) REVERT: A 924 ILE cc_start: 0.8365 (mp) cc_final: 0.8132 (mt) outliers start: 6 outliers final: 3 residues processed: 166 average time/residue: 0.1033 time to fit residues: 22.3312 Evaluate side-chains 92 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 1170 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 456 ASN ** A 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN A 622 GLN A 633 GLN ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 GLN A 772 GLN A 799 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN A 937 GLN A 959 GLN ** A1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1121 ASN A1148 GLN A1160 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.163955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.143661 restraints weight = 10855.276| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.34 r_work: 0.3640 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8546 Z= 0.108 Angle : 0.542 11.516 11570 Z= 0.283 Chirality : 0.044 0.151 1186 Planarity : 0.003 0.040 1528 Dihedral : 3.869 31.607 1159 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 2.02 % Allowed : 11.02 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.24), residues: 1025 helix: -0.57 (1.57), residues: 13 sheet: -0.05 (0.41), residues: 173 loop : -2.13 (0.19), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 931 TYR 0.018 0.001 TYR A1094 PHE 0.015 0.001 PHE A1075 TRP 0.014 0.001 TRP A 856 HIS 0.007 0.001 HIS A 650 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8546) covalent geometry : angle 0.54152 (11570) hydrogen bonds : bond 0.03063 ( 219) hydrogen bonds : angle 4.84471 ( 582) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.372 Fit side-chains REVERT: A 226 GLU cc_start: 0.6045 (pt0) cc_final: 0.5759 (pt0) REVERT: A 228 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7734 (mm-30) REVERT: A 445 LEU cc_start: 0.7434 (tp) cc_final: 0.7042 (tt) REVERT: A 658 GLN cc_start: 0.8324 (mm-40) cc_final: 0.7977 (mt0) REVERT: A 918 LYS cc_start: 0.7925 (tttt) cc_final: 0.7526 (ttmm) REVERT: A 1056 TYR cc_start: 0.8105 (m-80) cc_final: 0.7837 (m-80) outliers start: 18 outliers final: 13 residues processed: 118 average time/residue: 0.0904 time to fit residues: 14.9689 Evaluate side-chains 101 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1084 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS A 421 HIS ** A 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 GLN A 937 GLN A1082 GLN A1089 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.149771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.128956 restraints weight = 10939.779| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.38 r_work: 0.3450 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8546 Z= 0.205 Angle : 0.663 15.688 11570 Z= 0.346 Chirality : 0.047 0.164 1186 Planarity : 0.004 0.041 1528 Dihedral : 5.148 32.398 1158 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 2.81 % Allowed : 12.37 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.25), residues: 1025 helix: -0.40 (1.57), residues: 13 sheet: 0.04 (0.35), residues: 234 loop : -2.05 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 290 TYR 0.017 0.002 TYR A1094 PHE 0.024 0.002 PHE A1075 TRP 0.018 0.002 TRP A 513 HIS 0.007 0.002 HIS A 556 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 8546) covalent geometry : angle 0.66348 (11570) hydrogen bonds : bond 0.04396 ( 219) hydrogen bonds : angle 5.20202 ( 582) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.320 Fit side-chains REVERT: A 228 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8003 (mm-30) REVERT: A 398 TYR cc_start: 0.8457 (m-80) cc_final: 0.8251 (m-10) REVERT: A 487 LEU cc_start: 0.8697 (mm) cc_final: 0.8400 (mm) REVERT: A 658 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8341 (tp40) REVERT: A 783 ARG cc_start: 0.8301 (ptt90) cc_final: 0.8079 (ttp-110) REVERT: A 918 LYS cc_start: 0.7667 (tttt) cc_final: 0.7339 (ttmm) REVERT: A 920 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7647 (mmp) REVERT: A 943 ARG cc_start: 0.8424 (tmm-80) cc_final: 0.7609 (ttm170) REVERT: A 1155 GLN cc_start: 0.7826 (tp-100) cc_final: 0.7489 (tp40) outliers start: 25 outliers final: 15 residues processed: 117 average time/residue: 0.0874 time to fit residues: 14.1991 Evaluate side-chains 97 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 798 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1084 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 52 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 94 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS ** A 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 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 = 0.3755 r_free = 0.3755 target = 0.145540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.125633 restraints weight = 11306.467| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.29 r_work: 0.3413 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8546 Z= 0.222 Angle : 0.689 15.546 11570 Z= 0.359 Chirality : 0.048 0.164 1186 Planarity : 0.005 0.046 1528 Dihedral : 5.510 32.750 1158 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer: Outliers : 3.04 % Allowed : 14.74 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.25), residues: 1025 helix: -1.01 (1.44), residues: 13 sheet: 0.01 (0.35), residues: 233 loop : -2.09 (0.20), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 388 TYR 0.017 0.002 TYR A1094 PHE 0.024 0.002 PHE A1075 TRP 0.018 0.002 TRP A 513 HIS 0.008 0.002 HIS A 766 Details of bonding type rmsd covalent geometry : bond 0.00537 ( 8546) covalent geometry : angle 0.68903 (11570) hydrogen bonds : bond 0.04591 ( 219) hydrogen bonds : angle 5.26200 ( 582) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.369 Fit side-chains REVERT: A 918 LYS cc_start: 0.7887 (tttt) cc_final: 0.7527 (ttmm) REVERT: A 943 ARG cc_start: 0.8403 (tmm-80) cc_final: 0.7703 (ttp-170) REVERT: A 1155 GLN cc_start: 0.7853 (tp-100) cc_final: 0.7577 (tp40) outliers start: 27 outliers final: 22 residues processed: 109 average time/residue: 0.0821 time to fit residues: 12.6350 Evaluate side-chains 98 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 798 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1084 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 60 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 6 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS ** A 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 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 = 0.3818 r_free = 0.3818 target = 0.151277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.131530 restraints weight = 11092.589| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.30 r_work: 0.3495 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8546 Z= 0.104 Angle : 0.571 13.809 11570 Z= 0.295 Chirality : 0.044 0.158 1186 Planarity : 0.003 0.043 1528 Dihedral : 4.737 32.932 1158 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 2.47 % Allowed : 15.41 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.25), residues: 1025 helix: -0.23 (1.59), residues: 13 sheet: 0.02 (0.35), residues: 244 loop : -1.92 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 388 TYR 0.012 0.001 TYR A1094 PHE 0.010 0.001 PHE A 229 TRP 0.010 0.001 TRP A 513 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 8546) covalent geometry : angle 0.57078 (11570) hydrogen bonds : bond 0.03147 ( 219) hydrogen bonds : angle 4.93854 ( 582) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.216 Fit side-chains REVERT: A 918 LYS cc_start: 0.7874 (tttt) cc_final: 0.7564 (ttmm) REVERT: A 920 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7512 (mmp) REVERT: A 943 ARG cc_start: 0.8307 (tmm-80) cc_final: 0.7545 (ttm170) REVERT: A 1155 GLN cc_start: 0.7826 (tp-100) cc_final: 0.7557 (tp40) outliers start: 22 outliers final: 14 residues processed: 109 average time/residue: 0.0841 time to fit residues: 12.9839 Evaluate side-chains 98 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 82 optimal weight: 0.0470 chunk 5 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 HIS ** A 854 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 = 0.3782 r_free = 0.3782 target = 0.148146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.128546 restraints weight = 11086.581| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.26 r_work: 0.3451 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8546 Z= 0.153 Angle : 0.611 14.701 11570 Z= 0.317 Chirality : 0.046 0.158 1186 Planarity : 0.004 0.044 1528 Dihedral : 4.959 34.345 1158 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer: Outliers : 2.25 % Allowed : 16.99 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.25), residues: 1025 helix: -0.40 (1.54), residues: 13 sheet: 0.30 (0.36), residues: 230 loop : -1.92 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 388 TYR 0.017 0.001 TYR A1094 PHE 0.018 0.001 PHE A1075 TRP 0.014 0.001 TRP A 513 HIS 0.010 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8546) covalent geometry : angle 0.61113 (11570) hydrogen bonds : bond 0.03802 ( 219) hydrogen bonds : angle 4.99128 ( 582) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.319 Fit side-chains REVERT: A 240 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7888 (tp40) REVERT: A 918 LYS cc_start: 0.7879 (tttt) cc_final: 0.7561 (ttmm) REVERT: A 920 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7584 (mmp) REVERT: A 943 ARG cc_start: 0.8308 (tmm-80) cc_final: 0.7631 (ttp-170) REVERT: A 1155 GLN cc_start: 0.7828 (tp-100) cc_final: 0.7566 (tp40) outliers start: 20 outliers final: 15 residues processed: 96 average time/residue: 0.0831 time to fit residues: 11.1915 Evaluate side-chains 97 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 76 optimal weight: 0.0980 chunk 5 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS ** A 854 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 = 0.3806 r_free = 0.3806 target = 0.150231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.130769 restraints weight = 11135.847| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.26 r_work: 0.3480 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8546 Z= 0.116 Angle : 0.576 14.041 11570 Z= 0.299 Chirality : 0.044 0.156 1186 Planarity : 0.003 0.043 1528 Dihedral : 4.771 34.016 1158 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 2.47 % Allowed : 17.44 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.25), residues: 1025 helix: -0.08 (1.61), residues: 13 sheet: 0.54 (0.37), residues: 224 loop : -1.89 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 388 TYR 0.013 0.001 TYR A1094 PHE 0.011 0.001 PHE A1075 TRP 0.010 0.001 TRP A 513 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8546) covalent geometry : angle 0.57648 (11570) hydrogen bonds : bond 0.03311 ( 219) hydrogen bonds : angle 4.87769 ( 582) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.340 Fit side-chains REVERT: A 769 LYS cc_start: 0.8332 (tppt) cc_final: 0.8037 (mtmm) REVERT: A 918 LYS cc_start: 0.7912 (tttt) cc_final: 0.7581 (ttmm) REVERT: A 943 ARG cc_start: 0.8291 (tmm-80) cc_final: 0.7627 (ttp-170) REVERT: A 962 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6966 (pm20) REVERT: A 1155 GLN cc_start: 0.7823 (tp-100) cc_final: 0.7568 (tp40) outliers start: 22 outliers final: 17 residues processed: 106 average time/residue: 0.0926 time to fit residues: 13.5988 Evaluate side-chains 104 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 962 GLU Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 74 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 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 = 0.3772 r_free = 0.3772 target = 0.147232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.127922 restraints weight = 11132.631| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.23 r_work: 0.3442 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8546 Z= 0.170 Angle : 0.628 14.882 11570 Z= 0.326 Chirality : 0.046 0.160 1186 Planarity : 0.004 0.045 1528 Dihedral : 5.046 34.809 1158 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 2.36 % Allowed : 17.89 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.25), residues: 1025 helix: -0.17 (1.56), residues: 13 sheet: 0.24 (0.36), residues: 231 loop : -1.90 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 388 TYR 0.017 0.001 TYR A1094 PHE 0.018 0.001 PHE A1075 TRP 0.015 0.001 TRP A 513 HIS 0.006 0.001 HIS A 766 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 8546) covalent geometry : angle 0.62819 (11570) hydrogen bonds : bond 0.03967 ( 219) hydrogen bonds : angle 4.99665 ( 582) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.239 Fit side-chains REVERT: A 918 LYS cc_start: 0.8026 (tttt) cc_final: 0.7648 (ttmm) REVERT: A 943 ARG cc_start: 0.8305 (tmm-80) cc_final: 0.7650 (ttp-170) REVERT: A 962 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6990 (pm20) REVERT: A 1155 GLN cc_start: 0.7846 (tp-100) cc_final: 0.7593 (tp40) outliers start: 21 outliers final: 16 residues processed: 104 average time/residue: 0.0904 time to fit residues: 13.5639 Evaluate side-chains 99 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 962 GLU Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 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 234 HIS ** A 854 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 = 0.3810 r_free = 0.3810 target = 0.150635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.131396 restraints weight = 11024.387| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.24 r_work: 0.3485 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8546 Z= 0.111 Angle : 0.579 13.940 11570 Z= 0.300 Chirality : 0.044 0.157 1186 Planarity : 0.003 0.042 1528 Dihedral : 4.730 34.208 1158 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 1.91 % Allowed : 18.79 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.25), residues: 1025 helix: 0.12 (1.61), residues: 13 sheet: 0.54 (0.37), residues: 224 loop : -1.85 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 388 TYR 0.013 0.001 TYR A1094 PHE 0.010 0.001 PHE A 229 TRP 0.010 0.001 TRP A 513 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8546) covalent geometry : angle 0.57927 (11570) hydrogen bonds : bond 0.03179 ( 219) hydrogen bonds : angle 4.85395 ( 582) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.309 Fit side-chains REVERT: A 769 LYS cc_start: 0.8298 (tppt) cc_final: 0.7999 (mtmm) REVERT: A 815 ASP cc_start: 0.7316 (m-30) cc_final: 0.6998 (t0) REVERT: A 826 ASP cc_start: 0.7906 (t0) cc_final: 0.7703 (t0) REVERT: A 918 LYS cc_start: 0.8028 (tttt) cc_final: 0.7635 (ttmm) REVERT: A 943 ARG cc_start: 0.8291 (tmm-80) cc_final: 0.7637 (ttp-170) REVERT: A 962 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6964 (pm20) outliers start: 17 outliers final: 16 residues processed: 104 average time/residue: 0.0964 time to fit residues: 13.9772 Evaluate side-chains 103 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 962 GLU Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 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 = 0.3812 r_free = 0.3812 target = 0.150799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.131581 restraints weight = 11003.169| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.23 r_work: 0.3491 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8546 Z= 0.109 Angle : 0.575 13.711 11570 Z= 0.298 Chirality : 0.044 0.156 1186 Planarity : 0.003 0.042 1528 Dihedral : 4.670 34.435 1158 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 1.91 % Allowed : 18.79 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.25), residues: 1025 helix: 0.25 (1.64), residues: 13 sheet: 0.59 (0.37), residues: 224 loop : -1.81 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 388 TYR 0.013 0.001 TYR A1094 PHE 0.014 0.001 PHE A 175 TRP 0.009 0.001 TRP A 513 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8546) covalent geometry : angle 0.57537 (11570) hydrogen bonds : bond 0.03162 ( 219) hydrogen bonds : angle 4.82444 ( 582) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.376 Fit side-chains REVERT: A 769 LYS cc_start: 0.8298 (tppt) cc_final: 0.7999 (mtmm) REVERT: A 815 ASP cc_start: 0.7335 (m-30) cc_final: 0.7001 (t0) REVERT: A 918 LYS cc_start: 0.8017 (tttt) cc_final: 0.7625 (ttmm) REVERT: A 943 ARG cc_start: 0.8283 (tmm-80) cc_final: 0.7630 (ttp-170) REVERT: A 962 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6960 (pm20) outliers start: 17 outliers final: 16 residues processed: 101 average time/residue: 0.0925 time to fit residues: 13.2298 Evaluate side-chains 103 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 962 GLU Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 11 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 10 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 HIS ** A 854 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 = 0.3818 r_free = 0.3818 target = 0.151348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.132142 restraints weight = 11050.977| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.23 r_work: 0.3501 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8546 Z= 0.107 Angle : 0.573 13.503 11570 Z= 0.298 Chirality : 0.044 0.155 1186 Planarity : 0.003 0.042 1528 Dihedral : 4.612 34.483 1158 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 1.91 % Allowed : 18.67 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.26), residues: 1025 helix: 0.34 (1.64), residues: 13 sheet: 0.76 (0.37), residues: 219 loop : -1.81 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 388 TYR 0.014 0.001 TYR A 591 PHE 0.012 0.001 PHE A 175 TRP 0.009 0.001 TRP A 513 HIS 0.004 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8546) covalent geometry : angle 0.57323 (11570) hydrogen bonds : bond 0.03084 ( 219) hydrogen bonds : angle 4.77001 ( 582) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2036.51 seconds wall clock time: 35 minutes 36.64 seconds (2136.64 seconds total)