Starting phenix.real_space_refine on Wed Mar 12 10:42:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ptx_13642/03_2025/7ptx_13642.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ptx_13642/03_2025/7ptx_13642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ptx_13642/03_2025/7ptx_13642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ptx_13642/03_2025/7ptx_13642.map" model { file = "/net/cci-nas-00/data/ceres_data/7ptx_13642/03_2025/7ptx_13642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ptx_13642/03_2025/7ptx_13642.cif" } resolution = 4.03 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= 0.001 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 23 5.16 5 C 4829 2.51 5 N 1334 2.21 5 O 1467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7653 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7653 Classifications: {'peptide': 1000} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 31, 'TRANS': 968} Chain breaks: 2 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 156 Time building chain proxies: 5.62, per 1000 atoms: 0.73 Number of scatterers: 7653 At special positions: 0 Unit cell: (123.3, 127.8, 90, 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 23 16.00 O 1467 8.00 N 1334 7.00 C 4829 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: 2.09 Conformation dependent library (CDL) restraints added in 1.2 seconds 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1898 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 2 sheets defined 64.2% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 48 through 57 removed outlier: 3.585A pdb=" N VAL A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 62 removed outlier: 4.185A pdb=" N GLY A 61 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA A 62 " --> pdb=" O ILE A 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 58 through 62' Processing helix chain 'A' and resid 66 through 77 removed outlier: 3.708A pdb=" N ALA A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 Processing helix chain 'A' and resid 90 through 109 Processing helix chain 'A' and resid 119 through 147 removed outlier: 4.018A pdb=" N GLU A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 142 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 147 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 151 removed outlier: 3.506A pdb=" N ILE A 151 " --> pdb=" O ILE A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 151' Processing helix chain 'A' and resid 157 through 178 removed outlier: 3.739A pdb=" N GLU A 175 " --> pdb=" O ASN A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 196 through 204 removed outlier: 4.502A pdb=" N SER A 204 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 225 removed outlier: 3.821A pdb=" N LEU A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A 225 " --> pdb=" O ASN A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 269 Processing helix chain 'A' and resid 272 through 296 Processing helix chain 'A' and resid 304 through 320 removed outlier: 3.750A pdb=" N ARG A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 348 removed outlier: 3.763A pdb=" N ASN A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS A 335 " --> pdb=" O GLN A 331 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 468 Processing helix chain 'A' and resid 470 through 484 removed outlier: 4.159A pdb=" N GLY A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 506 Processing helix chain 'A' and resid 508 through 515 Processing helix chain 'A' and resid 517 through 524 removed outlier: 3.544A pdb=" N LEU A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 541 through 550 removed outlier: 3.878A pdb=" N GLU A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 571 removed outlier: 3.686A pdb=" N ALA A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 584 Processing helix chain 'A' and resid 601 through 608 removed outlier: 3.975A pdb=" N ILE A 605 " --> pdb=" O HIS A 602 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N THR A 606 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 618 removed outlier: 4.369A pdb=" N ARG A 613 " --> pdb=" O SER A 609 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN A 617 " --> pdb=" O ARG A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 640 Processing helix chain 'A' and resid 642 through 653 removed outlier: 4.250A pdb=" N ASN A 653 " --> pdb=" O LEU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 676 Processing helix chain 'A' and resid 677 through 687 Processing helix chain 'A' and resid 702 through 710 Processing helix chain 'A' and resid 713 through 723 removed outlier: 4.051A pdb=" N ARG A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 735 removed outlier: 4.400A pdb=" N ALA A 734 " --> pdb=" O ARG A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 745 removed outlier: 3.884A pdb=" N LEU A 740 " --> pdb=" O THR A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 756 Processing helix chain 'A' and resid 769 through 777 removed outlier: 3.883A pdb=" N LEU A 773 " --> pdb=" O THR A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 789 removed outlier: 4.254A pdb=" N GLN A 784 " --> pdb=" O THR A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 811 removed outlier: 4.173A pdb=" N PHE A 806 " --> pdb=" O THR A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 835 through 844 removed outlier: 3.840A pdb=" N GLU A 839 " --> pdb=" O MET A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 857 removed outlier: 4.094A pdb=" N VAL A 849 " --> pdb=" O HIS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 861 Processing helix chain 'A' and resid 870 through 878 Processing helix chain 'A' and resid 879 through 889 Processing helix chain 'A' and resid 893 through 897 removed outlier: 3.582A pdb=" N ASN A 897 " --> pdb=" O ASN A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 908 removed outlier: 3.753A pdb=" N SER A 908 " --> pdb=" O LEU A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 914 through 921 Processing helix chain 'A' and resid 935 through 943 removed outlier: 3.695A pdb=" N PHE A 943 " --> pdb=" O LEU A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 955 removed outlier: 4.015A pdb=" N VAL A 949 " --> pdb=" O HIS A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 980 removed outlier: 3.741A pdb=" N CYS A 975 " --> pdb=" O TYR A 971 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP A 976 " --> pdb=" O HIS A 972 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 977 " --> pdb=" O ALA A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 992 Processing helix chain 'A' and resid 999 through 1007 removed outlier: 3.738A pdb=" N GLU A1003 " --> pdb=" O SER A 999 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1021 Processing helix chain 'A' and resid 1034 through 1042 Processing helix chain 'A' and resid 1054 through 1065 removed outlier: 3.920A pdb=" N VAL A1059 " --> pdb=" O GLU A1055 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL A1060 " --> pdb=" O ARG A1056 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A1062 " --> pdb=" O ASP A1058 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 369 through 373 Processing sheet with id=AA2, first strand: chain 'A' and resid 402 through 403 388 hydrogen bonds defined for protein. 1140 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: 2.34 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2577 1.34 - 1.46: 1185 1.46 - 1.58: 3976 1.58 - 1.70: 0 1.70 - 1.82: 39 Bond restraints: 7777 Sorted by residual: bond pdb=" C ASN A 419 " pdb=" N PRO A 420 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.12e-02 7.97e+03 4.32e+00 bond pdb=" CB PRO A 737 " pdb=" CG PRO A 737 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.30e+00 bond pdb=" C THR A 782 " pdb=" N PRO A 783 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.46e+00 bond pdb=" CG MET A 283 " pdb=" SD MET A 283 " ideal model delta sigma weight residual 1.803 1.778 0.025 2.50e-02 1.60e+03 9.65e-01 bond pdb=" CG GLU A 876 " pdb=" CD GLU A 876 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 9.64e-01 ... (remaining 7772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 10186 1.79 - 3.59: 277 3.59 - 5.38: 50 5.38 - 7.18: 19 7.18 - 8.97: 5 Bond angle restraints: 10537 Sorted by residual: angle pdb=" CA PRO A 737 " pdb=" N PRO A 737 " pdb=" CD PRO A 737 " ideal model delta sigma weight residual 112.00 106.07 5.93 1.40e+00 5.10e-01 1.79e+01 angle pdb=" N VAL A 65 " pdb=" CA VAL A 65 " pdb=" C VAL A 65 " ideal model delta sigma weight residual 112.80 108.59 4.21 1.15e+00 7.56e-01 1.34e+01 angle pdb=" C ILE A 832 " pdb=" N ASN A 833 " pdb=" CA ASN A 833 " ideal model delta sigma weight residual 122.46 127.43 -4.97 1.41e+00 5.03e-01 1.24e+01 angle pdb=" C HIS A 282 " pdb=" N MET A 283 " pdb=" CA MET A 283 " ideal model delta sigma weight residual 121.14 115.15 5.99 1.75e+00 3.27e-01 1.17e+01 angle pdb=" N GLU A 876 " pdb=" CA GLU A 876 " pdb=" CB GLU A 876 " ideal model delta sigma weight residual 110.39 116.05 -5.66 1.66e+00 3.63e-01 1.16e+01 ... (remaining 10532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 4195 16.46 - 32.91: 441 32.91 - 49.37: 80 49.37 - 65.83: 13 65.83 - 82.28: 7 Dihedral angle restraints: 4736 sinusoidal: 1814 harmonic: 2922 Sorted by residual: dihedral pdb=" CA LYS A 934 " pdb=" C LYS A 934 " pdb=" N SER A 935 " pdb=" CA SER A 935 " ideal model delta harmonic sigma weight residual 180.00 -157.28 -22.72 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA LYS A 699 " pdb=" C LYS A 699 " pdb=" N ASN A 700 " pdb=" CA ASN A 700 " ideal model delta harmonic sigma weight residual 180.00 157.60 22.40 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA THR A 992 " pdb=" C THR A 992 " pdb=" N LEU A 993 " pdb=" CA LEU A 993 " ideal model delta harmonic sigma weight residual -180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 4733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 719 0.034 - 0.068: 353 0.068 - 0.102: 105 0.102 - 0.135: 36 0.135 - 0.169: 11 Chirality restraints: 1224 Sorted by residual: chirality pdb=" CA GLU A 134 " pdb=" N GLU A 134 " pdb=" C GLU A 134 " pdb=" CB GLU A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CA PRO A 737 " pdb=" N PRO A 737 " pdb=" C PRO A 737 " pdb=" CB PRO A 737 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CB VAL A 56 " pdb=" CA VAL A 56 " pdb=" CG1 VAL A 56 " pdb=" CG2 VAL A 56 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 1221 not shown) Planarity restraints: 1381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 736 " -0.064 5.00e-02 4.00e+02 9.42e-02 1.42e+01 pdb=" N PRO A 737 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 737 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 737 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 441 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.20e+00 pdb=" N PRO A 442 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 442 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 442 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 632 " -0.033 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO A 633 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 633 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 633 " -0.028 5.00e-02 4.00e+02 ... (remaining 1378 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 883 2.74 - 3.28: 9100 3.28 - 3.82: 13154 3.82 - 4.36: 15240 4.36 - 4.90: 23646 Nonbonded interactions: 62023 Sorted by model distance: nonbonded pdb=" O PHE A 367 " pdb=" NZ LYS A 407 " model vdw 2.203 3.120 nonbonded pdb=" NH2 ARG A 512 " pdb=" O PHE A 544 " model vdw 2.209 3.120 nonbonded pdb=" O GLU A 493 " pdb=" NZ LYS A 527 " model vdw 2.243 3.120 nonbonded pdb=" O ARG A 610 " pdb=" OG1 THR A 614 " model vdw 2.250 3.040 nonbonded pdb=" O ASN A 439 " pdb=" NZ LYS A 441 " model vdw 2.252 3.120 ... (remaining 62018 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.360 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.980 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 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 : 0.003 0.076 7777 Z= 0.215 Angle : 0.756 8.972 10537 Z= 0.411 Chirality : 0.045 0.169 1224 Planarity : 0.005 0.094 1381 Dihedral : 14.083 82.282 2838 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.26), residues: 994 helix: -0.39 (0.21), residues: 575 sheet: -3.62 (0.77), residues: 35 loop : -2.46 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 384 HIS 0.004 0.001 HIS A 972 PHE 0.020 0.001 PHE A 290 TYR 0.025 0.002 TYR A 951 ARG 0.005 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 666 MET cc_start: 0.7947 (ppp) cc_final: 0.6675 (ppp) REVERT: A 901 ASN cc_start: 0.8547 (p0) cc_final: 0.8330 (p0) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1772 time to fit residues: 29.1420 Evaluate side-chains 90 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 78 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 ASN ** 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 = 0.3947 r_free = 0.3947 target = 0.080072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.068478 restraints weight = 42783.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.070088 restraints weight = 28398.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.071249 restraints weight = 20735.356| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7777 Z= 0.195 Angle : 0.659 6.464 10537 Z= 0.350 Chirality : 0.043 0.153 1224 Planarity : 0.005 0.059 1381 Dihedral : 5.492 21.941 1058 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 0.25 % Allowed : 8.19 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.26), residues: 994 helix: -0.20 (0.21), residues: 590 sheet: -3.45 (0.74), residues: 35 loop : -2.45 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 384 HIS 0.008 0.001 HIS A 459 PHE 0.017 0.001 PHE A 290 TYR 0.022 0.002 TYR A 872 ARG 0.007 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.7655 (tpt) cc_final: 0.7043 (tpp) REVERT: A 95 ASP cc_start: 0.8419 (t0) cc_final: 0.8207 (t0) REVERT: A 127 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8242 (pp20) REVERT: A 283 MET cc_start: 0.9199 (pmm) cc_final: 0.8692 (pmm) REVERT: A 666 MET cc_start: 0.8272 (ppp) cc_final: 0.7578 (ppp) REVERT: A 805 HIS cc_start: 0.7519 (m90) cc_final: 0.7260 (m90) REVERT: A 1009 HIS cc_start: 0.8216 (m90) cc_final: 0.7976 (m90) REVERT: A 1011 ASP cc_start: 0.9024 (p0) cc_final: 0.8509 (p0) REVERT: A 1012 LEU cc_start: 0.9347 (mm) cc_final: 0.9064 (mm) outliers start: 2 outliers final: 0 residues processed: 124 average time/residue: 0.1769 time to fit residues: 30.8646 Evaluate side-chains 92 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 97 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.080039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.068337 restraints weight = 43257.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.069955 restraints weight = 28721.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.071123 restraints weight = 20889.950| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7777 Z= 0.199 Angle : 0.659 5.937 10537 Z= 0.351 Chirality : 0.044 0.153 1224 Planarity : 0.005 0.055 1381 Dihedral : 5.433 21.012 1058 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 0.37 % Allowed : 7.20 % Favored : 92.43 % 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: -1.56 (0.26), residues: 994 helix: -0.06 (0.21), residues: 588 sheet: -3.10 (0.79), residues: 35 loop : -2.39 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 701 HIS 0.005 0.001 HIS A 459 PHE 0.018 0.001 PHE A 290 TYR 0.016 0.001 TYR A 130 ARG 0.008 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.7924 (ttt) cc_final: 0.7563 (tmm) REVERT: A 95 ASP cc_start: 0.8466 (t0) cc_final: 0.8249 (t0) REVERT: A 283 MET cc_start: 0.9110 (pmm) cc_final: 0.8665 (pmm) REVERT: A 461 ASP cc_start: 0.7628 (m-30) cc_final: 0.7347 (m-30) REVERT: A 494 MET cc_start: 0.6925 (mpp) cc_final: 0.6680 (mpp) REVERT: A 666 MET cc_start: 0.8188 (ppp) cc_final: 0.7915 (ppp) REVERT: A 675 LEU cc_start: 0.8157 (mm) cc_final: 0.7860 (mm) REVERT: A 776 MET cc_start: 0.8916 (mpp) cc_final: 0.8682 (mpp) REVERT: A 805 HIS cc_start: 0.7595 (m90) cc_final: 0.7305 (m90) REVERT: A 851 MET cc_start: 0.8914 (mtm) cc_final: 0.8592 (mtt) REVERT: A 865 MET cc_start: 0.7796 (tpp) cc_final: 0.7244 (tpp) REVERT: A 1009 HIS cc_start: 0.8174 (m90) cc_final: 0.7903 (m90) REVERT: A 1011 ASP cc_start: 0.8988 (p0) cc_final: 0.8624 (p0) REVERT: A 1012 LEU cc_start: 0.9355 (mm) cc_final: 0.9114 (mm) outliers start: 3 outliers final: 0 residues processed: 123 average time/residue: 0.1703 time to fit residues: 29.7779 Evaluate side-chains 92 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 59 optimal weight: 0.0000 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 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 = 0.3967 r_free = 0.3967 target = 0.080763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.068969 restraints weight = 43087.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.070576 restraints weight = 28660.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.071748 restraints weight = 20932.622| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7777 Z= 0.186 Angle : 0.655 7.229 10537 Z= 0.344 Chirality : 0.043 0.154 1224 Planarity : 0.005 0.058 1381 Dihedral : 5.347 21.004 1058 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.25 % Allowed : 4.71 % Favored : 95.04 % 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: -1.32 (0.26), residues: 994 helix: 0.14 (0.21), residues: 578 sheet: -2.79 (0.83), residues: 35 loop : -2.26 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 701 HIS 0.004 0.001 HIS A 282 PHE 0.019 0.001 PHE A 290 TYR 0.025 0.002 TYR A 872 ARG 0.009 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 1.122 Fit side-chains REVERT: A 95 ASP cc_start: 0.8382 (t0) cc_final: 0.8154 (t0) REVERT: A 283 MET cc_start: 0.9205 (pmm) cc_final: 0.8459 (pmm) REVERT: A 317 LYS cc_start: 0.8795 (pttm) cc_final: 0.8565 (mmmm) REVERT: A 461 ASP cc_start: 0.7696 (m-30) cc_final: 0.7410 (m-30) REVERT: A 666 MET cc_start: 0.8117 (ppp) cc_final: 0.7839 (ppp) REVERT: A 776 MET cc_start: 0.8925 (mpp) cc_final: 0.8671 (mpp) REVERT: A 805 HIS cc_start: 0.7535 (m90) cc_final: 0.7219 (m90) REVERT: A 851 MET cc_start: 0.8851 (mtm) cc_final: 0.8550 (mtt) REVERT: A 865 MET cc_start: 0.7701 (tpp) cc_final: 0.7162 (tpp) REVERT: A 934 LYS cc_start: 0.7844 (tttm) cc_final: 0.6742 (tttm) REVERT: A 1009 HIS cc_start: 0.8156 (m90) cc_final: 0.7876 (m90) REVERT: A 1011 ASP cc_start: 0.9063 (p0) cc_final: 0.8594 (p0) REVERT: A 1012 LEU cc_start: 0.9392 (mm) cc_final: 0.9117 (mm) outliers start: 2 outliers final: 0 residues processed: 127 average time/residue: 0.2123 time to fit residues: 36.9846 Evaluate side-chains 95 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 64 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 46 optimal weight: 0.0030 chunk 90 optimal weight: 0.0470 chunk 47 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.4688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.080900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.069197 restraints weight = 42714.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.070839 restraints weight = 28474.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.072006 restraints weight = 20705.912| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7777 Z= 0.182 Angle : 0.654 6.712 10537 Z= 0.345 Chirality : 0.044 0.163 1224 Planarity : 0.005 0.054 1381 Dihedral : 5.235 20.326 1058 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 0.12 % Allowed : 4.59 % Favored : 95.29 % 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: -1.32 (0.26), residues: 994 helix: 0.11 (0.21), residues: 586 sheet: -2.40 (0.89), residues: 35 loop : -2.30 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 701 HIS 0.004 0.001 HIS A 772 PHE 0.019 0.001 PHE A 290 TYR 0.020 0.001 TYR A 130 ARG 0.007 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.7228 (ttt) cc_final: 0.6680 (tmm) REVERT: A 95 ASP cc_start: 0.8453 (t0) cc_final: 0.8198 (t0) REVERT: A 461 ASP cc_start: 0.7741 (m-30) cc_final: 0.7466 (m-30) REVERT: A 666 MET cc_start: 0.8077 (ppp) cc_final: 0.7758 (ppp) REVERT: A 675 LEU cc_start: 0.8108 (mm) cc_final: 0.7585 (mm) REVERT: A 776 MET cc_start: 0.8825 (mpp) cc_final: 0.8612 (mpp) REVERT: A 851 MET cc_start: 0.8864 (mtm) cc_final: 0.8566 (mtt) REVERT: A 852 LEU cc_start: 0.8516 (pp) cc_final: 0.8176 (tt) REVERT: A 865 MET cc_start: 0.7679 (tpp) cc_final: 0.7047 (tpp) REVERT: A 918 PHE cc_start: 0.8832 (m-10) cc_final: 0.8501 (m-10) REVERT: A 1009 HIS cc_start: 0.8102 (m90) cc_final: 0.7784 (m90) REVERT: A 1011 ASP cc_start: 0.8963 (p0) cc_final: 0.8491 (p0) REVERT: A 1012 LEU cc_start: 0.9376 (mm) cc_final: 0.9070 (mm) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.1801 time to fit residues: 31.4952 Evaluate side-chains 97 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 0.0870 chunk 91 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 36 optimal weight: 0.0770 chunk 37 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN A 897 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.081638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.069803 restraints weight = 43527.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.071500 restraints weight = 28442.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.072735 restraints weight = 20498.140| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7777 Z= 0.179 Angle : 0.667 8.156 10537 Z= 0.349 Chirality : 0.044 0.155 1224 Planarity : 0.005 0.052 1381 Dihedral : 5.183 20.617 1058 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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: -1.27 (0.26), residues: 994 helix: 0.14 (0.21), residues: 584 sheet: -1.90 (0.96), residues: 33 loop : -2.31 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 701 HIS 0.004 0.001 HIS A 459 PHE 0.019 0.001 PHE A 290 TYR 0.038 0.001 TYR A1015 ARG 0.006 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.7089 (ttt) cc_final: 0.6626 (tmm) REVERT: A 95 ASP cc_start: 0.8394 (t0) cc_final: 0.8140 (t0) REVERT: A 283 MET cc_start: 0.8978 (pmm) cc_final: 0.8556 (pmm) REVERT: A 461 ASP cc_start: 0.7742 (m-30) cc_final: 0.7479 (m-30) REVERT: A 675 LEU cc_start: 0.8079 (mm) cc_final: 0.7574 (mm) REVERT: A 776 MET cc_start: 0.8813 (mpp) cc_final: 0.8609 (mpp) REVERT: A 805 HIS cc_start: 0.7488 (m170) cc_final: 0.7285 (m90) REVERT: A 851 MET cc_start: 0.8887 (mtm) cc_final: 0.8600 (mtt) REVERT: A 852 LEU cc_start: 0.8507 (pp) cc_final: 0.8116 (tt) REVERT: A 865 MET cc_start: 0.7701 (tpp) cc_final: 0.7146 (tpp) REVERT: A 934 LYS cc_start: 0.8001 (tttm) cc_final: 0.7036 (tttm) REVERT: A 1009 HIS cc_start: 0.8132 (m90) cc_final: 0.7829 (m90) REVERT: A 1011 ASP cc_start: 0.8937 (p0) cc_final: 0.8522 (p0) REVERT: A 1012 LEU cc_start: 0.9326 (mm) cc_final: 0.9069 (mm) REVERT: A 1015 TYR cc_start: 0.8974 (m-80) cc_final: 0.8632 (m-80) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1914 time to fit residues: 33.3097 Evaluate side-chains 97 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 ASN ** 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 = 0.3964 r_free = 0.3964 target = 0.080841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.069064 restraints weight = 43991.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.070718 restraints weight = 29344.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.071889 restraints weight = 21431.047| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7777 Z= 0.196 Angle : 0.676 8.491 10537 Z= 0.355 Chirality : 0.044 0.180 1224 Planarity : 0.005 0.053 1381 Dihedral : 5.194 19.935 1058 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.26), residues: 994 helix: 0.08 (0.21), residues: 583 sheet: -1.79 (0.97), residues: 33 loop : -2.30 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 701 HIS 0.004 0.001 HIS A 500 PHE 0.017 0.001 PHE A 907 TYR 0.027 0.002 TYR A1015 ARG 0.009 0.001 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.7202 (ttt) cc_final: 0.6665 (tmm) REVERT: A 95 ASP cc_start: 0.8454 (t0) cc_final: 0.8198 (t0) REVERT: A 461 ASP cc_start: 0.7745 (m-30) cc_final: 0.7485 (m-30) REVERT: A 851 MET cc_start: 0.8936 (mtm) cc_final: 0.8670 (mtt) REVERT: A 865 MET cc_start: 0.7748 (tpp) cc_final: 0.7222 (tpp) REVERT: A 901 ASN cc_start: 0.8915 (p0) cc_final: 0.8633 (p0) REVERT: A 934 LYS cc_start: 0.8160 (tttm) cc_final: 0.7201 (tttm) REVERT: A 1011 ASP cc_start: 0.8951 (p0) cc_final: 0.8598 (p0) REVERT: A 1012 LEU cc_start: 0.9347 (mm) cc_final: 0.9084 (mm) REVERT: A 1015 TYR cc_start: 0.9061 (m-80) cc_final: 0.8769 (m-80) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2202 time to fit residues: 36.2097 Evaluate side-chains 91 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 86 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 0.0870 chunk 42 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 ASN ** 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 = 0.3969 r_free = 0.3969 target = 0.081102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.069236 restraints weight = 44469.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.070860 restraints weight = 29760.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.072049 restraints weight = 21855.165| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7777 Z= 0.201 Angle : 0.700 8.545 10537 Z= 0.365 Chirality : 0.045 0.192 1224 Planarity : 0.005 0.053 1381 Dihedral : 5.183 20.125 1058 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: -1.34 (0.26), residues: 994 helix: 0.02 (0.21), residues: 583 sheet: -1.66 (0.98), residues: 33 loop : -2.25 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 701 HIS 0.004 0.001 HIS A 459 PHE 0.027 0.002 PHE A 918 TYR 0.024 0.002 TYR A1015 ARG 0.005 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.6997 (ttt) cc_final: 0.6556 (tmm) REVERT: A 95 ASP cc_start: 0.8385 (t0) cc_final: 0.8135 (t0) REVERT: A 461 ASP cc_start: 0.7732 (m-30) cc_final: 0.7477 (m-30) REVERT: A 666 MET cc_start: 0.8033 (ppp) cc_final: 0.7821 (ppp) REVERT: A 851 MET cc_start: 0.8904 (mtm) cc_final: 0.8636 (mtt) REVERT: A 865 MET cc_start: 0.7711 (tpp) cc_final: 0.7238 (tpp) REVERT: A 934 LYS cc_start: 0.8098 (tttm) cc_final: 0.7163 (tttm) REVERT: A 1009 HIS cc_start: 0.8045 (m90) cc_final: 0.7818 (m90) REVERT: A 1011 ASP cc_start: 0.8966 (p0) cc_final: 0.8461 (p0) REVERT: A 1012 LEU cc_start: 0.9347 (mm) cc_final: 0.9082 (mm) REVERT: A 1015 TYR cc_start: 0.9025 (m-80) cc_final: 0.8705 (m-80) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1827 time to fit residues: 29.9634 Evaluate side-chains 94 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 46 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 64 optimal weight: 0.1980 chunk 55 optimal weight: 0.0870 chunk 99 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 GLN ** A 897 ASN ** 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 = 0.3990 r_free = 0.3990 target = 0.081810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.069812 restraints weight = 43226.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.071536 restraints weight = 28422.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.072765 restraints weight = 20565.761| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 7777 Z= 0.190 Angle : 0.698 9.102 10537 Z= 0.360 Chirality : 0.044 0.177 1224 Planarity : 0.005 0.052 1381 Dihedral : 5.079 19.981 1058 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: -1.23 (0.26), residues: 994 helix: 0.09 (0.21), residues: 584 sheet: -1.39 (1.02), residues: 33 loop : -2.18 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 701 HIS 0.004 0.001 HIS A 459 PHE 0.022 0.002 PHE A 918 TYR 0.022 0.001 TYR A1015 ARG 0.005 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.6934 (ttt) cc_final: 0.6516 (tmm) REVERT: A 95 ASP cc_start: 0.8433 (t0) cc_final: 0.8179 (t0) REVERT: A 339 SER cc_start: 0.8852 (m) cc_final: 0.8641 (m) REVERT: A 776 MET cc_start: 0.8720 (mmm) cc_final: 0.8508 (mpp) REVERT: A 865 MET cc_start: 0.7572 (tpp) cc_final: 0.7107 (tpp) REVERT: A 901 ASN cc_start: 0.8878 (p0) cc_final: 0.8601 (p0) REVERT: A 934 LYS cc_start: 0.8079 (tttm) cc_final: 0.7167 (tttm) REVERT: A 988 TYR cc_start: 0.8978 (t80) cc_final: 0.8630 (t80) REVERT: A 1009 HIS cc_start: 0.8023 (m90) cc_final: 0.7804 (m90) REVERT: A 1011 ASP cc_start: 0.8996 (p0) cc_final: 0.8420 (p0) REVERT: A 1012 LEU cc_start: 0.9335 (mm) cc_final: 0.9066 (mm) REVERT: A 1015 TYR cc_start: 0.9013 (m-80) cc_final: 0.8714 (m-80) REVERT: A 1050 SER cc_start: 0.8990 (m) cc_final: 0.8772 (p) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1871 time to fit residues: 30.6244 Evaluate side-chains 94 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 91 optimal weight: 0.3980 chunk 72 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 93 optimal weight: 0.0270 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.081453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.069417 restraints weight = 43719.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.071143 restraints weight = 28646.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.072369 restraints weight = 20735.400| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 7777 Z= 0.200 Angle : 0.706 10.013 10537 Z= 0.363 Chirality : 0.044 0.189 1224 Planarity : 0.005 0.052 1381 Dihedral : 5.112 20.052 1058 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -1.26 (0.26), residues: 994 helix: 0.05 (0.21), residues: 583 sheet: -0.82 (1.22), residues: 23 loop : -2.22 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 701 HIS 0.009 0.001 HIS A 213 PHE 0.025 0.002 PHE A 918 TYR 0.022 0.002 TYR A1015 ARG 0.005 0.000 ARG A 613 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.6995 (ttt) cc_final: 0.6521 (tmm) REVERT: A 95 ASP cc_start: 0.8464 (t0) cc_final: 0.8206 (t0) REVERT: A 339 SER cc_start: 0.8889 (m) cc_final: 0.8650 (m) REVERT: A 606 THR cc_start: 0.5036 (m) cc_final: 0.4698 (t) REVERT: A 666 MET cc_start: 0.7937 (ppp) cc_final: 0.7733 (ppp) REVERT: A 675 LEU cc_start: 0.8183 (mm) cc_final: 0.7865 (mm) REVERT: A 776 MET cc_start: 0.8791 (mmm) cc_final: 0.8470 (mpp) REVERT: A 816 PHE cc_start: 0.8566 (t80) cc_final: 0.8309 (t80) REVERT: A 848 ILE cc_start: 0.8784 (mp) cc_final: 0.8558 (mp) REVERT: A 865 MET cc_start: 0.7581 (tpp) cc_final: 0.7107 (tpp) REVERT: A 901 ASN cc_start: 0.8900 (p0) cc_final: 0.8615 (p0) REVERT: A 934 LYS cc_start: 0.8128 (tttm) cc_final: 0.7200 (tttm) REVERT: A 1009 HIS cc_start: 0.8033 (m90) cc_final: 0.7806 (m90) REVERT: A 1011 ASP cc_start: 0.9066 (p0) cc_final: 0.8384 (p0) REVERT: A 1012 LEU cc_start: 0.9337 (mm) cc_final: 0.9042 (mm) REVERT: A 1015 TYR cc_start: 0.9034 (m-80) cc_final: 0.8643 (m-80) REVERT: A 1050 SER cc_start: 0.8991 (m) cc_final: 0.8775 (p) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2267 time to fit residues: 36.7265 Evaluate side-chains 99 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 25 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 55 optimal weight: 0.0270 chunk 59 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 ASN ** 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 = 0.3977 r_free = 0.3977 target = 0.081507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.069719 restraints weight = 44649.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.071335 restraints weight = 29742.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.072506 restraints weight = 21789.827| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 7777 Z= 0.210 Angle : 0.709 10.442 10537 Z= 0.368 Chirality : 0.045 0.189 1224 Planarity : 0.005 0.053 1381 Dihedral : 5.142 20.769 1058 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -1.25 (0.26), residues: 994 helix: 0.07 (0.21), residues: 584 sheet: -0.83 (1.21), residues: 23 loop : -2.21 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 701 HIS 0.007 0.001 HIS A 213 PHE 0.025 0.002 PHE A 918 TYR 0.021 0.002 TYR A1015 ARG 0.005 0.000 ARG A 613 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3112.42 seconds wall clock time: 55 minutes 42.33 seconds (3342.33 seconds total)