Starting phenix.real_space_refine on Wed Mar 12 22:36:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h8b_34541/03_2025/8h8b_34541.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h8b_34541/03_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_34541/03_2025/8h8b_34541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h8b_34541/03_2025/8h8b_34541.map" model { file = "/net/cci-nas-00/data/ceres_data/8h8b_34541/03_2025/8h8b_34541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h8b_34541/03_2025/8h8b_34541.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.76, per 1000 atoms: 0.57 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: 1.97 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.82 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: 4.55 Time building geometry restraints manager: 2.41 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: 1.200 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.460 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.290 ------------------------------------------------------------------------------- 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= 0.096 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 (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: -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 TRP 0.003 0.000 TRP A 438 HIS 0.004 0.000 HIS A 444 PHE 0.006 0.000 PHE A 267 TYR 0.009 0.001 TYR A 242 ARG 0.001 0.000 ARG A 979 *********************** 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 : 0.860 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: 0.2566 time to fit residues: 55.6080 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 : 0.977 ------------------------------------------------------------------------------- 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 86 optimal weight: 3.9990 chunk 77 optimal weight: 0.0060 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 421 HIS A 456 ASN A 529 HIS A 585 GLN A 622 GLN A 633 GLN ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN 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 A1082 GLN A1089 ASN A1148 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.151714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130729 restraints weight = 10849.723| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.39 r_work: 0.3475 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8546 Z= 0.329 Angle : 0.681 15.361 11570 Z= 0.358 Chirality : 0.048 0.163 1186 Planarity : 0.005 0.044 1528 Dihedral : 5.049 31.028 1159 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Rotamer: Outliers : 2.92 % Allowed : 10.91 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.45 (0.24), residues: 1025 helix: -1.19 (1.46), residues: 13 sheet: -0.27 (0.35), residues: 236 loop : -2.27 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 856 HIS 0.009 0.002 HIS A 556 PHE 0.027 0.002 PHE A1075 TYR 0.023 0.002 TYR A1094 ARG 0.004 0.001 ARG A 436 *********************** 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 139 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.892 Fit side-chains REVERT: A 228 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8023 (mm-30) REVERT: A 487 LEU cc_start: 0.8660 (mm) cc_final: 0.8330 (mm) REVERT: A 658 GLN cc_start: 0.8582 (mm-40) cc_final: 0.7989 (mt0) REVERT: A 783 ARG cc_start: 0.8302 (ptt90) cc_final: 0.8076 (ttp-110) REVERT: A 918 LYS cc_start: 0.7820 (tttt) cc_final: 0.7477 (ttmm) REVERT: A 1142 GLN cc_start: 0.6613 (mt0) cc_final: 0.6380 (mt0) outliers start: 26 outliers final: 17 residues processed: 128 average time/residue: 0.2179 time to fit residues: 39.2940 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 : 0.929 ------------------------------------------------------------------------------- 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 207 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 362 ILE 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 768 THR Chi-restraints excluded: chain A residue 798 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 967 SER 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 95 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 0.0770 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- 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** A 868 GLN A 937 GLN A1121 ASN A1160 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.154383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.134276 restraints weight = 11076.147| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.32 r_work: 0.3530 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3262 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= 0.147 Angle : 0.554 13.356 11570 Z= 0.288 Chirality : 0.044 0.157 1186 Planarity : 0.003 0.041 1528 Dihedral : 4.471 30.662 1158 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.02 % Allowed : 13.39 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.25), residues: 1025 helix: -0.49 (1.59), residues: 13 sheet: -0.15 (0.35), residues: 247 loop : -2.01 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 177 HIS 0.005 0.001 HIS A 650 PHE 0.009 0.001 PHE A 229 TYR 0.011 0.001 TYR A1094 ARG 0.005 0.000 ARG A 388 *********************** 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 107 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.882 Fit side-chains REVERT: A 487 LEU cc_start: 0.8650 (mm) cc_final: 0.8303 (mm) REVERT: A 658 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8203 (mt0) REVERT: A 783 ARG cc_start: 0.8205 (ptt90) cc_final: 0.7976 (ttp-110) REVERT: A 918 LYS cc_start: 0.7801 (tttt) cc_final: 0.7478 (ttmm) REVERT: A 1155 GLN cc_start: 0.7853 (tp-100) cc_final: 0.7545 (tp40) outliers start: 18 outliers final: 12 residues processed: 104 average time/residue: 0.1818 time to fit residues: 27.3064 Evaluate side-chains 94 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 804 THR 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 1132 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 42 optimal weight: 5.9990 chunk 85 optimal weight: 0.0970 chunk 31 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 23 optimal weight: 0.0870 chunk 27 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 overall best weight: 2.0362 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.147653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127787 restraints weight = 11089.715| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.27 r_work: 0.3444 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8546 Z= 0.297 Angle : 0.645 15.406 11570 Z= 0.335 Chirality : 0.047 0.164 1186 Planarity : 0.004 0.042 1528 Dihedral : 5.132 32.534 1158 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.10 % Favored : 87.90 % Rotamer: Outliers : 2.81 % Allowed : 14.06 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.06 (0.25), residues: 1025 helix: -0.44 (1.55), residues: 13 sheet: 0.12 (0.35), residues: 233 loop : -2.04 (0.20), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 177 HIS 0.006 0.001 HIS A 766 PHE 0.020 0.002 PHE A1075 TYR 0.017 0.002 TYR A1094 ARG 0.004 0.001 ARG A 388 *********************** 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 107 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 1.066 Fit side-chains REVERT: A 283 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8486 (mt) REVERT: A 398 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.8286 (m-10) REVERT: A 591 TYR cc_start: 0.8536 (m-10) cc_final: 0.8325 (m-10) REVERT: A 658 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8417 (tp40) REVERT: A 918 LYS cc_start: 0.7746 (tttt) cc_final: 0.7397 (ttmm) REVERT: A 943 ARG cc_start: 0.8468 (tmm-80) cc_final: 0.7895 (ttt180) REVERT: A 1155 GLN cc_start: 0.7901 (tp-100) cc_final: 0.7632 (tp40) outliers start: 25 outliers final: 18 residues processed: 102 average time/residue: 0.2513 time to fit residues: 36.1997 Evaluate side-chains 97 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 398 TYR 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 804 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.150636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.130847 restraints weight = 10964.996| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.30 r_work: 0.3482 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3785 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= 0.168 Angle : 0.575 14.159 11570 Z= 0.297 Chirality : 0.044 0.157 1186 Planarity : 0.003 0.044 1528 Dihedral : 4.768 32.655 1158 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 2.59 % Allowed : 15.30 % 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 (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: -1.93 (0.25), residues: 1025 helix: -0.04 (1.61), residues: 13 sheet: -0.01 (0.35), residues: 247 loop : -1.90 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 513 HIS 0.004 0.001 HIS A 198 PHE 0.010 0.001 PHE A1075 TYR 0.013 0.001 TYR A1094 ARG 0.002 0.000 ARG A 388 *********************** 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 110 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 1.212 Fit side-chains REVERT: A 398 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.8084 (m-10) REVERT: A 598 ARG cc_start: 0.7595 (ttm170) cc_final: 0.7394 (tpp-160) REVERT: A 918 LYS cc_start: 0.7767 (tttt) cc_final: 0.7391 (ttmm) REVERT: A 943 ARG cc_start: 0.8424 (tmm-80) cc_final: 0.7625 (ttp-170) REVERT: A 1155 GLN cc_start: 0.7846 (tp-100) cc_final: 0.7572 (tp40) outliers start: 23 outliers final: 17 residues processed: 103 average time/residue: 0.2675 time to fit residues: 39.9427 Evaluate side-chains 98 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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 398 TYR 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 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 76 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.150030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130440 restraints weight = 11035.697| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.27 r_work: 0.3476 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8546 Z= 0.183 Angle : 0.576 14.289 11570 Z= 0.298 Chirality : 0.044 0.156 1186 Planarity : 0.003 0.044 1528 Dihedral : 4.738 33.579 1158 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 2.14 % Allowed : 16.76 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.25), residues: 1025 helix: 0.06 (1.62), residues: 13 sheet: 0.31 (0.36), residues: 233 loop : -1.88 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 513 HIS 0.005 0.001 HIS A 234 PHE 0.014 0.001 PHE A1075 TYR 0.014 0.001 TYR A1094 ARG 0.002 0.000 ARG A 388 *********************** 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 105 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.800 Fit side-chains REVERT: A 149 GLU cc_start: 0.5829 (pm20) cc_final: 0.5324 (pm20) REVERT: A 240 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7557 (tm-30) REVERT: A 283 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8453 (mt) REVERT: A 398 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.8084 (m-10) REVERT: A 598 ARG cc_start: 0.7584 (ttm170) cc_final: 0.7382 (tpp-160) REVERT: A 918 LYS cc_start: 0.7735 (tttt) cc_final: 0.7360 (ttmm) REVERT: A 943 ARG cc_start: 0.8421 (tmm-80) cc_final: 0.7638 (ttp-170) REVERT: A 1155 GLN cc_start: 0.7828 (tp-100) cc_final: 0.7557 (tp40) outliers start: 19 outliers final: 14 residues processed: 99 average time/residue: 0.2188 time to fit residues: 30.9843 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 : 0.998 ------------------------------------------------------------------------------- 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 398 TYR 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 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 7 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 97 optimal weight: 0.0040 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.151125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.131232 restraints weight = 11096.993| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.32 r_work: 0.3481 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8546 Z= 0.166 Angle : 0.566 13.748 11570 Z= 0.293 Chirality : 0.044 0.156 1186 Planarity : 0.003 0.042 1528 Dihedral : 4.655 33.997 1158 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 2.47 % Allowed : 16.99 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.25), residues: 1025 helix: 0.22 (1.66), residues: 13 sheet: 0.50 (0.37), residues: 227 loop : -1.85 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 513 HIS 0.004 0.001 HIS A 444 PHE 0.012 0.001 PHE A1075 TYR 0.013 0.001 TYR A1094 ARG 0.007 0.000 ARG A 388 *********************** 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 104 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.935 Fit side-chains REVERT: A 398 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.8006 (m-10) REVERT: A 769 LYS cc_start: 0.8316 (tppt) cc_final: 0.8019 (mtmm) REVERT: A 918 LYS cc_start: 0.7800 (tttt) cc_final: 0.7424 (ttmm) REVERT: A 943 ARG cc_start: 0.8361 (tmm-80) cc_final: 0.7611 (ttp-170) REVERT: A 1155 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7600 (tp40) outliers start: 22 outliers final: 16 residues processed: 98 average time/residue: 0.2039 time to fit residues: 28.3543 Evaluate side-chains 95 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 398 TYR 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 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 14 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.148126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.128545 restraints weight = 11079.325| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.26 r_work: 0.3447 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8546 Z= 0.238 Angle : 0.611 14.814 11570 Z= 0.316 Chirality : 0.046 0.160 1186 Planarity : 0.004 0.045 1528 Dihedral : 4.989 34.192 1158 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Rotamer: Outliers : 2.59 % Allowed : 17.21 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.25), residues: 1025 helix: 0.13 (1.63), residues: 13 sheet: 0.33 (0.36), residues: 233 loop : -1.84 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 513 HIS 0.005 0.001 HIS A 766 PHE 0.017 0.001 PHE A1075 TYR 0.016 0.001 TYR A1094 ARG 0.007 0.000 ARG A 388 *********************** 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 106 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.869 Fit side-chains REVERT: A 240 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7839 (tp40) REVERT: A 283 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8497 (mt) REVERT: A 398 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.8079 (m-10) REVERT: A 815 ASP cc_start: 0.7360 (m-30) cc_final: 0.7038 (t0) REVERT: A 918 LYS cc_start: 0.7797 (tttt) cc_final: 0.7423 (ttmm) REVERT: A 943 ARG cc_start: 0.8360 (tmm-80) cc_final: 0.7605 (ttp-170) REVERT: A 962 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7107 (pt0) REVERT: A 1155 GLN cc_start: 0.7864 (tp-100) cc_final: 0.7613 (tp40) outliers start: 23 outliers final: 18 residues processed: 101 average time/residue: 0.1896 time to fit residues: 27.9823 Evaluate side-chains 102 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 240 GLN 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 398 TYR 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 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 32 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.145295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.125413 restraints weight = 11292.723| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.30 r_work: 0.3408 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 8546 Z= 0.366 Angle : 0.695 15.884 11570 Z= 0.362 Chirality : 0.048 0.171 1186 Planarity : 0.004 0.047 1528 Dihedral : 5.481 34.441 1158 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 2.92 % Allowed : 16.87 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.25), residues: 1025 helix: -0.32 (1.53), residues: 13 sheet: 0.09 (0.36), residues: 235 loop : -1.94 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 377 HIS 0.008 0.002 HIS A 766 PHE 0.022 0.002 PHE A1075 TYR 0.017 0.002 TYR A1094 ARG 0.008 0.001 ARG A 388 *********************** 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 105 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.946 Fit side-chains REVERT: A 283 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8530 (mt) REVERT: A 398 TYR cc_start: 0.8684 (OUTLIER) cc_final: 0.8177 (m-10) REVERT: A 918 LYS cc_start: 0.7883 (tttt) cc_final: 0.7514 (ttmm) REVERT: A 943 ARG cc_start: 0.8419 (tmm-80) cc_final: 0.7684 (ttp-170) REVERT: A 962 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7031 (pm20) REVERT: A 1155 GLN cc_start: 0.7836 (tp-100) cc_final: 0.7580 (tp40) outliers start: 26 outliers final: 21 residues processed: 101 average time/residue: 0.1825 time to fit residues: 26.9175 Evaluate side-chains 95 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 398 TYR 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 606 VAL Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 798 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 962 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 11 optimal weight: 0.0980 chunk 65 optimal weight: 4.9990 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 173 ASN A 234 HIS ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.146400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.127006 restraints weight = 11113.843| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.24 r_work: 0.3435 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8546 Z= 0.265 Angle : 0.643 15.008 11570 Z= 0.334 Chirality : 0.046 0.162 1186 Planarity : 0.004 0.047 1528 Dihedral : 5.247 33.962 1158 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer: Outliers : 2.70 % Allowed : 17.44 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.25), residues: 1025 helix: -0.36 (1.52), residues: 13 sheet: -0.07 (0.35), residues: 242 loop : -1.91 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 513 HIS 0.005 0.001 HIS A 198 PHE 0.017 0.001 PHE A1075 TYR 0.016 0.001 TYR A1094 ARG 0.007 0.000 ARG A 388 ********************** 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 101 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.953 Fit side-chains REVERT: A 283 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8497 (mt) REVERT: A 398 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.8053 (m-10) REVERT: A 918 LYS cc_start: 0.7864 (tttt) cc_final: 0.7482 (ttmm) REVERT: A 943 ARG cc_start: 0.8343 (tmm-80) cc_final: 0.7613 (ttp-170) REVERT: A 962 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7103 (pt0) REVERT: A 1155 GLN cc_start: 0.7824 (tp-100) cc_final: 0.7561 (tp40) outliers start: 24 outliers final: 20 residues processed: 96 average time/residue: 0.1873 time to fit residues: 26.5847 Evaluate side-chains 97 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 307 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 398 TYR 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 606 VAL Chi-restraints excluded: chain A residue 609 SER 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 47 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 0.0370 chunk 3 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 234 HIS ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.149079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.129831 restraints weight = 11236.829| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.23 r_work: 0.3471 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4215 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= 0.176 Angle : 0.594 14.231 11570 Z= 0.308 Chirality : 0.045 0.156 1186 Planarity : 0.003 0.045 1528 Dihedral : 4.933 33.868 1158 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 2.70 % Allowed : 17.44 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.25), residues: 1025 helix: -0.07 (1.58), residues: 13 sheet: 0.33 (0.37), residues: 228 loop : -1.87 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 513 HIS 0.009 0.001 HIS A 234 PHE 0.011 0.001 PHE A1075 TYR 0.013 0.001 TYR A1094 ARG 0.006 0.000 ARG A 388 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4289.80 seconds wall clock time: 76 minutes 28.61 seconds (4588.61 seconds total)