Starting phenix.real_space_refine on Wed Feb 12 21:29:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h8b_34541/02_2025/8h8b_34541.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h8b_34541/02_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_34541/02_2025/8h8b_34541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h8b_34541/02_2025/8h8b_34541.map" model { file = "/net/cci-nas-00/data/ceres_data/8h8b_34541/02_2025/8h8b_34541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h8b_34541/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.79, 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: 2.08 Conformation dependent library (CDL) restraints added in 988.7 milliseconds 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: 1.24 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: 3.49 Time building geometry restraints manager: 2.31 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.080 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.020 ------------------------------------------------------------------------------- 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 : 0.958 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: 0.2633 time to fit residues: 56.8567 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 : 1.032 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130725 restraints weight = 10849.731| |-----------------------------------------------------------------------------| 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: 4.93 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 31.029 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 : 0.938 Fit side-chains REVERT: A 228 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8022 (mm-30) REVERT: A 487 LEU cc_start: 0.8659 (mm) cc_final: 0.8329 (mm) REVERT: A 658 GLN cc_start: 0.8580 (mm-40) cc_final: 0.7985 (mt0) REVERT: A 783 ARG cc_start: 0.8298 (ptt90) cc_final: 0.8072 (ttp-110) REVERT: A 918 LYS cc_start: 0.7813 (tttt) cc_final: 0.7468 (ttmm) REVERT: A 1142 GLN cc_start: 0.6598 (mt0) cc_final: 0.6365 (mt0) outliers start: 26 outliers final: 17 residues processed: 128 average time/residue: 0.1965 time to fit residues: 35.3266 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 : 0.968 ------------------------------------------------------------------------------- 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: 0.7980 chunk 82 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 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 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 = 0.3850 r_free = 0.3850 target = 0.153782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.133616 restraints weight = 11092.842| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.33 r_work: 0.3521 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8546 Z= 0.154 Angle : 0.559 13.528 11570 Z= 0.290 Chirality : 0.044 0.158 1186 Planarity : 0.003 0.042 1528 Dihedral : 4.520 30.680 1158 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % 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: -2.12 (0.25), residues: 1025 helix: -0.50 (1.58), residues: 13 sheet: -0.16 (0.35), residues: 247 loop : -2.02 (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 0.012 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 106 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.911 Fit side-chains REVERT: A 487 LEU cc_start: 0.8652 (mm) cc_final: 0.8306 (mm) REVERT: A 658 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8197 (mt0) REVERT: A 783 ARG cc_start: 0.8219 (ptt90) cc_final: 0.7987 (ttp-110) REVERT: A 918 LYS cc_start: 0.7806 (tttt) cc_final: 0.7483 (ttmm) REVERT: A 1155 GLN cc_start: 0.7852 (tp-100) cc_final: 0.7542 (tp40) outliers start: 18 outliers final: 12 residues processed: 103 average time/residue: 0.1882 time to fit residues: 27.9514 Evaluate side-chains 93 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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: 0.8980 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 0.4980 chunk 27 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.151955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.132039 restraints weight = 10980.925| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.30 r_work: 0.3497 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8546 Z= 0.176 Angle : 0.567 13.914 11570 Z= 0.293 Chirality : 0.044 0.155 1186 Planarity : 0.003 0.041 1528 Dihedral : 4.573 32.712 1158 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 2.70 % Allowed : 13.39 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.25), residues: 1025 helix: -0.12 (1.60), residues: 13 sheet: -0.03 (0.35), residues: 247 loop : -1.94 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 177 HIS 0.004 0.001 HIS A 650 PHE 0.013 0.001 PHE A1075 TYR 0.014 0.001 TYR A1094 ARG 0.003 0.000 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 113 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.909 Fit side-chains REVERT: A 480 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.8073 (mt) REVERT: A 658 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8243 (mt0) REVERT: A 769 LYS cc_start: 0.8286 (tppt) cc_final: 0.7939 (mtmm) REVERT: A 783 ARG cc_start: 0.8242 (ptt90) cc_final: 0.8024 (ttp-110) REVERT: A 918 LYS cc_start: 0.7651 (tttt) cc_final: 0.7290 (ttmm) REVERT: A 943 ARG cc_start: 0.8224 (tmm-80) cc_final: 0.7578 (ttp-170) REVERT: A 1155 GLN cc_start: 0.7865 (tp-100) cc_final: 0.7582 (tp40) outliers start: 24 outliers final: 17 residues processed: 105 average time/residue: 0.1944 time to fit residues: 29.4018 Evaluate side-chains 99 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 480 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 784 VAL 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 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: 6.9990 chunk 69 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.148336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.128794 restraints weight = 11032.239| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.25 r_work: 0.3457 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8546 Z= 0.257 Angle : 0.624 15.169 11570 Z= 0.323 Chirality : 0.046 0.163 1186 Planarity : 0.004 0.043 1528 Dihedral : 5.046 32.956 1158 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 3.04 % Allowed : 14.51 % Favored : 82.45 % 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: -1.89 (0.25), residues: 1025 helix: -0.16 (1.57), residues: 13 sheet: 0.23 (0.36), residues: 233 loop : -1.92 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 513 HIS 0.006 0.001 HIS A 766 PHE 0.019 0.002 PHE A1075 TYR 0.016 0.001 TYR A1094 ARG 0.003 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 112 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.990 Fit side-chains REVERT: A 149 GLU cc_start: 0.5868 (pm20) cc_final: 0.5359 (pm20) REVERT: A 226 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6467 (pt0) REVERT: A 283 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8471 (mt) REVERT: A 398 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.8181 (m-10) REVERT: A 591 TYR cc_start: 0.8464 (m-10) cc_final: 0.8223 (m-10) REVERT: A 598 ARG cc_start: 0.7610 (ttm170) cc_final: 0.7400 (tpp-160) REVERT: A 918 LYS cc_start: 0.7768 (tttt) cc_final: 0.7397 (ttmm) REVERT: A 943 ARG cc_start: 0.8252 (tmm-80) cc_final: 0.7623 (ttp-170) REVERT: A 1155 GLN cc_start: 0.7872 (tp-100) cc_final: 0.7616 (tp40) outliers start: 27 outliers final: 17 residues processed: 107 average time/residue: 0.2047 time to fit residues: 31.3286 Evaluate side-chains 99 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 226 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 76 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS A 481 GLN ** 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 = 0.3739 r_free = 0.3739 target = 0.144363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.124863 restraints weight = 11183.863| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.25 r_work: 0.3395 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8546 Z= 0.369 Angle : 0.699 15.937 11570 Z= 0.363 Chirality : 0.049 0.170 1186 Planarity : 0.004 0.047 1528 Dihedral : 5.558 32.664 1158 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.39 % Favored : 87.61 % Rotamer: Outliers : 3.15 % Allowed : 16.09 % Favored : 80.76 % 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: -2.08 (0.25), residues: 1025 helix: -0.59 (1.47), residues: 13 sheet: -0.10 (0.35), residues: 240 loop : -1.99 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 513 HIS 0.008 0.002 HIS A 766 PHE 0.022 0.002 PHE A1075 TYR 0.018 0.002 TYR A1094 ARG 0.003 0.001 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 114 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.982 Fit side-chains REVERT: A 149 GLU cc_start: 0.5700 (pm20) cc_final: 0.5090 (pm20) REVERT: A 169 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8797 (p) REVERT: A 226 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6556 (pt0) REVERT: A 240 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.8013 (tp40) REVERT: A 283 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8534 (mt) REVERT: A 398 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.8124 (m-10) REVERT: A 918 LYS cc_start: 0.7846 (tttt) cc_final: 0.7475 (ttmm) REVERT: A 943 ARG cc_start: 0.8297 (tmm-80) cc_final: 0.7719 (ttp-170) REVERT: A 1155 GLN cc_start: 0.7852 (tp-100) cc_final: 0.7583 (tp40) outliers start: 28 outliers final: 21 residues processed: 109 average time/residue: 0.2060 time to fit residues: 31.8445 Evaluate side-chains 103 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 214 VAL Chi-restraints excluded: chain A residue 226 GLU 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 7 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 97 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.150822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.131150 restraints weight = 11084.953| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.30 r_work: 0.3488 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4066 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= 0.149 Angle : 0.575 13.856 11570 Z= 0.299 Chirality : 0.044 0.158 1186 Planarity : 0.003 0.045 1528 Dihedral : 4.817 33.173 1158 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 2.47 % Allowed : 17.55 % Favored : 79.98 % 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: 0.02 (1.60), residues: 13 sheet: 0.37 (0.36), residues: 229 loop : -1.90 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 513 HIS 0.009 0.001 HIS A 234 PHE 0.009 0.001 PHE A 954 TYR 0.011 0.001 TYR A1094 ARG 0.005 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 112 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.900 Fit side-chains REVERT: A 149 GLU cc_start: 0.5387 (pm20) cc_final: 0.4804 (pm20) REVERT: A 283 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8460 (mt) REVERT: A 398 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.8108 (m-10) REVERT: A 918 LYS cc_start: 0.7809 (tttt) cc_final: 0.7442 (ttmm) REVERT: A 943 ARG cc_start: 0.8275 (tmm-80) cc_final: 0.7614 (ttm170) REVERT: A 962 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7096 (pt0) outliers start: 22 outliers final: 16 residues processed: 108 average time/residue: 0.2093 time to fit residues: 31.9202 Evaluate side-chains 102 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 398 TYR Chi-restraints excluded: chain A residue 487 LEU 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 776 GLU Chi-restraints excluded: chain A residue 848 VAL 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 14 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 4 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.147877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.128375 restraints weight = 11084.258| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.24 r_work: 0.3449 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8546 Z= 0.233 Angle : 0.613 14.604 11570 Z= 0.318 Chirality : 0.046 0.157 1186 Planarity : 0.004 0.045 1528 Dihedral : 5.010 34.277 1158 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % Rotamer: Outliers : 2.59 % Allowed : 17.66 % 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 (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: -0.03 (1.57), residues: 13 sheet: 0.24 (0.36), residues: 236 loop : -1.87 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 513 HIS 0.005 0.001 HIS A 766 PHE 0.016 0.001 PHE A1075 TYR 0.015 0.001 TYR A1094 ARG 0.005 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 : 1.014 Fit side-chains REVERT: A 149 GLU cc_start: 0.5571 (pm20) cc_final: 0.5037 (pm20) REVERT: A 240 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7934 (tp40) REVERT: A 283 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8512 (mt) REVERT: A 398 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.8099 (m-10) REVERT: A 918 LYS cc_start: 0.7819 (tttt) cc_final: 0.7452 (ttmm) REVERT: A 943 ARG cc_start: 0.8275 (tmm-80) cc_final: 0.7693 (ttp-170) outliers start: 23 outliers final: 18 residues processed: 102 average time/residue: 0.1964 time to fit residues: 28.9287 Evaluate side-chains 101 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 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 776 GLU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 848 VAL 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: 5.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.147719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.128204 restraints weight = 11230.534| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.26 r_work: 0.3449 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4261 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= 0.236 Angle : 0.619 14.724 11570 Z= 0.322 Chirality : 0.046 0.161 1186 Planarity : 0.004 0.045 1528 Dihedral : 5.066 34.204 1158 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer: Outliers : 2.47 % Allowed : 18.22 % 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 (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: -1.83 (0.25), residues: 1025 helix: -0.09 (1.55), residues: 13 sheet: 0.18 (0.36), residues: 235 loop : -1.85 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 513 HIS 0.005 0.001 HIS A 198 PHE 0.016 0.001 PHE A1075 TYR 0.015 0.001 TYR A1094 ARG 0.004 0.000 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 103 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.917 Fit side-chains REVERT: A 149 GLU cc_start: 0.5591 (pm20) cc_final: 0.5037 (pm20) REVERT: A 283 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8509 (mt) REVERT: A 398 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.8115 (m-10) REVERT: A 918 LYS cc_start: 0.7868 (tttt) cc_final: 0.7505 (ttmm) REVERT: A 943 ARG cc_start: 0.8277 (tmm-80) cc_final: 0.7611 (ttm170) REVERT: A 962 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7000 (pm20) outliers start: 22 outliers final: 17 residues processed: 99 average time/residue: 0.2052 time to fit residues: 29.3989 Evaluate side-chains 101 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 776 GLU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 848 VAL 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 16 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.144909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.125486 restraints weight = 11174.013| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.24 r_work: 0.3415 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4484 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= 0.341 Angle : 0.686 15.807 11570 Z= 0.357 Chirality : 0.048 0.167 1186 Planarity : 0.004 0.048 1528 Dihedral : 5.491 33.951 1158 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.10 % Favored : 87.90 % Rotamer: Outliers : 2.47 % Allowed : 18.22 % Favored : 79.30 % 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: -2.03 (0.25), residues: 1025 helix: -0.41 (1.49), residues: 13 sheet: -0.12 (0.35), residues: 240 loop : -1.94 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 513 HIS 0.006 0.002 HIS A 766 PHE 0.021 0.002 PHE A1075 TYR 0.016 0.002 TYR A1094 ARG 0.004 0.001 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: 22 poor density : 79 time to evaluate : 0.910 Fit side-chains REVERT: A 149 GLU cc_start: 0.5665 (pm20) cc_final: 0.5127 (pm20) REVERT: A 283 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8522 (mt) REVERT: A 398 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.8178 (m-10) REVERT: A 918 LYS cc_start: 0.7872 (tttt) cc_final: 0.7504 (ttmm) REVERT: A 943 ARG cc_start: 0.8286 (tmm-80) cc_final: 0.7610 (ttp-170) REVERT: A 962 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7013 (pm20) outliers start: 22 outliers final: 19 residues processed: 98 average time/residue: 0.2243 time to fit residues: 30.8550 Evaluate side-chains 97 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 776 GLU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 848 VAL 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 47 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 35 optimal weight: 0.2980 chunk 3 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.147396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.127987 restraints weight = 11270.321| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.26 r_work: 0.3444 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8546 Z= 0.214 Angle : 0.627 14.761 11570 Z= 0.327 Chirality : 0.046 0.160 1186 Planarity : 0.004 0.046 1528 Dihedral : 5.201 33.806 1158 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer: Outliers : 2.59 % Allowed : 18.11 % Favored : 79.30 % 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: -1.90 (0.25), residues: 1025 helix: -0.25 (1.51), residues: 13 sheet: -0.05 (0.35), residues: 243 loop : -1.84 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 513 HIS 0.006 0.001 HIS A 234 PHE 0.014 0.001 PHE A1075 TYR 0.014 0.001 TYR A1094 ARG 0.008 0.000 ARG A 388 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4318.15 seconds wall clock time: 77 minutes 12.75 seconds (4632.75 seconds total)