Starting phenix.real_space_refine on Tue Feb 3 23:01:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ptx_13642/02_2026/7ptx_13642.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ptx_13642/02_2026/7ptx_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_13642/02_2026/7ptx_13642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ptx_13642/02_2026/7ptx_13642.map" model { file = "/net/cci-nas-00/data/ceres_data/7ptx_13642/02_2026/7ptx_13642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ptx_13642/02_2026/7ptx_13642.cif" } resolution = 4.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: {'ARG:plan': 9, 'GLU:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 5, 'PHE:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 156 Time building chain proxies: 1.68, per 1000 atoms: 0.22 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: 0.86 Conformation dependent library (CDL) restraints added in 333.9 milliseconds 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: 0.32 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: 1.37 Time building geometry restraints manager: 1.10 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: 4.500 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.410 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.880 ------------------------------------------------------------------------------- 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= 0.156 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.000 ARG A 512 TYR 0.025 0.002 TYR A 951 PHE 0.020 0.001 PHE A 290 TRP 0.003 0.001 TRP A 384 HIS 0.004 0.001 HIS A 972 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7777) covalent geometry : angle 0.75593 (10537) hydrogen bonds : bond 0.14129 ( 388) hydrogen bonds : angle 7.13394 ( 1140) *********************** 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 : 0.332 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: 0.8320 (p0) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0778 time to fit residues: 12.9651 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 : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.0370 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.081114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.069427 restraints weight = 42654.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.071084 restraints weight = 28329.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.072272 restraints weight = 20584.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.073132 restraints weight = 15948.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.073783 restraints weight = 13022.403| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7777 Z= 0.132 Angle : 0.656 6.621 10537 Z= 0.345 Chirality : 0.043 0.152 1224 Planarity : 0.005 0.059 1381 Dihedral : 5.407 21.711 1058 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 0.37 % Allowed : 8.19 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.26), residues: 994 helix: -0.12 (0.21), residues: 588 sheet: -3.28 (0.76), residues: 35 loop : -2.39 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 512 TYR 0.025 0.002 TYR A 872 PHE 0.017 0.001 PHE A 290 TRP 0.002 0.001 TRP A 384 HIS 0.008 0.001 HIS A 459 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7777) covalent geometry : angle 0.65555 (10537) hydrogen bonds : bond 0.04117 ( 388) hydrogen bonds : angle 5.66333 ( 1140) *********************** 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: 3 poor density : 122 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7603 (tpt) cc_final: 0.6988 (tpp) REVERT: A 95 ASP cc_start: 0.8366 (t0) cc_final: 0.8136 (t0) REVERT: A 127 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8211 (pp20) REVERT: A 283 MET cc_start: 0.9175 (pmm) cc_final: 0.8950 (pmm) REVERT: A 666 MET cc_start: 0.8210 (ppp) cc_final: 0.7561 (ppp) REVERT: A 805 HIS cc_start: 0.7544 (m90) cc_final: 0.7292 (m90) REVERT: A 1009 HIS cc_start: 0.8180 (m90) cc_final: 0.7935 (m90) REVERT: A 1011 ASP cc_start: 0.8959 (p0) cc_final: 0.8432 (p0) REVERT: A 1012 LEU cc_start: 0.9346 (mm) cc_final: 0.9088 (mm) outliers start: 3 outliers final: 1 residues processed: 124 average time/residue: 0.0820 time to fit residues: 14.4142 Evaluate side-chains 93 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 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 = 0.3950 r_free = 0.3950 target = 0.080092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.068298 restraints weight = 42924.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.069968 restraints weight = 28234.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.071161 restraints weight = 20384.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.072046 restraints weight = 15802.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.072674 restraints weight = 12873.797| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1531 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= 0.146 Angle : 0.660 6.315 10537 Z= 0.351 Chirality : 0.044 0.161 1224 Planarity : 0.005 0.056 1381 Dihedral : 5.400 20.691 1058 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 0.25 % Allowed : 6.58 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.26), residues: 994 helix: 0.02 (0.21), residues: 581 sheet: -3.00 (0.80), residues: 35 loop : -2.31 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 512 TYR 0.018 0.001 TYR A 130 PHE 0.018 0.001 PHE A 290 TRP 0.002 0.001 TRP A 701 HIS 0.005 0.001 HIS A 459 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7777) covalent geometry : angle 0.66011 (10537) hydrogen bonds : bond 0.04026 ( 388) hydrogen bonds : angle 5.59101 ( 1140) *********************** 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: 2 poor density : 122 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7590 (tpt) cc_final: 0.6967 (tpp) REVERT: A 87 MET cc_start: 0.7101 (ttp) cc_final: 0.6853 (tmm) REVERT: A 95 ASP cc_start: 0.8447 (t0) cc_final: 0.8228 (t0) REVERT: A 283 MET cc_start: 0.9097 (pmm) cc_final: 0.8655 (pmm) REVERT: A 461 ASP cc_start: 0.7538 (m-30) cc_final: 0.7273 (m-30) REVERT: A 494 MET cc_start: 0.6707 (mpp) cc_final: 0.6486 (mpp) REVERT: A 666 MET cc_start: 0.8169 (ppp) cc_final: 0.7877 (ppp) REVERT: A 776 MET cc_start: 0.8907 (mpp) cc_final: 0.8680 (mpp) REVERT: A 805 HIS cc_start: 0.7604 (m90) cc_final: 0.7351 (m90) REVERT: A 865 MET cc_start: 0.7754 (tpp) cc_final: 0.7208 (tpp) REVERT: A 1009 HIS cc_start: 0.8193 (m90) cc_final: 0.7936 (m90) REVERT: A 1011 ASP cc_start: 0.8944 (p0) cc_final: 0.8460 (p0) REVERT: A 1012 LEU cc_start: 0.9354 (mm) cc_final: 0.9078 (mm) outliers start: 2 outliers final: 0 residues processed: 123 average time/residue: 0.0824 time to fit residues: 14.4972 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 : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 0.0060 chunk 73 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 103 GLN ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 ASN A 921 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.079452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.067639 restraints weight = 44546.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.069232 restraints weight = 29387.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.070437 restraints weight = 21363.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.071271 restraints weight = 16620.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.071883 restraints weight = 13640.714| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7777 Z= 0.153 Angle : 0.669 6.915 10537 Z= 0.353 Chirality : 0.044 0.157 1224 Planarity : 0.005 0.063 1381 Dihedral : 5.471 21.005 1058 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.37 % Allowed : 5.96 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.26), residues: 994 helix: 0.01 (0.21), residues: 585 sheet: -2.97 (0.83), residues: 35 loop : -2.30 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 496 TYR 0.025 0.002 TYR A 951 PHE 0.020 0.002 PHE A 290 TRP 0.003 0.001 TRP A 701 HIS 0.005 0.001 HIS A 772 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 7777) covalent geometry : angle 0.66882 (10537) hydrogen bonds : bond 0.03971 ( 388) hydrogen bonds : angle 5.50788 ( 1140) *********************** 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 127 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.7757 (ttt) cc_final: 0.7271 (tmm) REVERT: A 95 ASP cc_start: 0.8422 (t0) cc_final: 0.8187 (t0) REVERT: A 283 MET cc_start: 0.9240 (pmm) cc_final: 0.9019 (pmm) REVERT: A 317 LYS cc_start: 0.8752 (pttm) cc_final: 0.8494 (mmmm) REVERT: A 666 MET cc_start: 0.8210 (ppp) cc_final: 0.7581 (ppp) REVERT: A 675 LEU cc_start: 0.8125 (mm) cc_final: 0.7613 (mm) REVERT: A 776 MET cc_start: 0.8972 (mpp) cc_final: 0.8705 (mpp) REVERT: A 805 HIS cc_start: 0.7602 (m90) cc_final: 0.7342 (m90) REVERT: A 835 MET cc_start: 0.8126 (mmp) cc_final: 0.7878 (mmp) REVERT: A 934 LYS cc_start: 0.7761 (tttm) cc_final: 0.6651 (tttm) REVERT: A 1009 HIS cc_start: 0.8234 (m90) cc_final: 0.7988 (m90) REVERT: A 1011 ASP cc_start: 0.9095 (p0) cc_final: 0.8621 (p0) REVERT: A 1012 LEU cc_start: 0.9393 (mm) cc_final: 0.9104 (mm) REVERT: A 1015 TYR cc_start: 0.9025 (m-80) cc_final: 0.8791 (m-80) outliers start: 3 outliers final: 1 residues processed: 126 average time/residue: 0.0933 time to fit residues: 16.0774 Evaluate side-chains 93 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 93 optimal weight: 0.0270 chunk 78 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 0.0270 chunk 12 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.080553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.068604 restraints weight = 43349.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.070323 restraints weight = 28294.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.071542 restraints weight = 20390.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.072464 restraints weight = 15722.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.073097 restraints weight = 12731.410| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7777 Z= 0.132 Angle : 0.670 7.867 10537 Z= 0.354 Chirality : 0.044 0.163 1224 Planarity : 0.005 0.054 1381 Dihedral : 5.303 20.737 1058 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 0.12 % Allowed : 4.34 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.26), residues: 994 helix: 0.13 (0.21), residues: 579 sheet: -2.71 (0.86), residues: 35 loop : -2.17 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 496 TYR 0.020 0.001 TYR A 130 PHE 0.020 0.001 PHE A 290 TRP 0.002 0.001 TRP A 384 HIS 0.005 0.001 HIS A 772 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7777) covalent geometry : angle 0.67007 (10537) hydrogen bonds : bond 0.03842 ( 388) hydrogen bonds : angle 5.50980 ( 1140) *********************** 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 : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ASP cc_start: 0.8387 (t0) cc_final: 0.8145 (t0) REVERT: A 461 ASP cc_start: 0.7706 (m-30) cc_final: 0.7434 (m-30) REVERT: A 675 LEU cc_start: 0.8089 (mm) cc_final: 0.7558 (mm) REVERT: A 805 HIS cc_start: 0.7616 (m90) cc_final: 0.7275 (m90) REVERT: A 852 LEU cc_start: 0.8491 (pp) cc_final: 0.8225 (tt) REVERT: A 865 MET cc_start: 0.7675 (tpp) cc_final: 0.7112 (tpp) REVERT: A 901 ASN cc_start: 0.8752 (p0) cc_final: 0.8444 (p0) REVERT: A 1009 HIS cc_start: 0.8050 (m90) cc_final: 0.7721 (m90) REVERT: A 1011 ASP cc_start: 0.9063 (p0) cc_final: 0.8363 (p0) REVERT: A 1012 LEU cc_start: 0.9387 (mm) cc_final: 0.8975 (mm) REVERT: A 1015 TYR cc_start: 0.9011 (m-80) cc_final: 0.8675 (m-80) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.0927 time to fit residues: 15.9080 Evaluate side-chains 101 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3951 r_free = 0.3951 target = 0.080175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.068465 restraints weight = 44167.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.070080 restraints weight = 29162.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.071234 restraints weight = 21229.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.072076 restraints weight = 16537.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.072712 restraints weight = 13536.113| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7777 Z= 0.143 Angle : 0.679 7.918 10537 Z= 0.354 Chirality : 0.044 0.154 1224 Planarity : 0.005 0.053 1381 Dihedral : 5.317 20.615 1058 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.26), residues: 994 helix: 0.07 (0.21), residues: 583 sheet: -2.29 (0.94), residues: 33 loop : -2.23 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 496 TYR 0.015 0.001 TYR A 130 PHE 0.030 0.002 PHE A 918 TRP 0.003 0.001 TRP A 701 HIS 0.004 0.001 HIS A 500 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7777) covalent geometry : angle 0.67872 (10537) hydrogen bonds : bond 0.03837 ( 388) hydrogen bonds : angle 5.44669 ( 1140) *********************** 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 : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.6992 (ttt) cc_final: 0.6544 (tmm) REVERT: A 95 ASP cc_start: 0.8406 (t0) cc_final: 0.8146 (t0) REVERT: A 461 ASP cc_start: 0.7572 (m-30) cc_final: 0.7313 (m-30) REVERT: A 675 LEU cc_start: 0.8152 (mm) cc_final: 0.7855 (mm) REVERT: A 776 MET cc_start: 0.8842 (mpp) cc_final: 0.8624 (mpp) REVERT: A 805 HIS cc_start: 0.7573 (m90) cc_final: 0.7245 (m90) REVERT: A 865 MET cc_start: 0.7661 (tpp) cc_final: 0.7107 (tpp) REVERT: A 1009 HIS cc_start: 0.8084 (m90) cc_final: 0.7770 (m90) REVERT: A 1011 ASP cc_start: 0.9035 (p0) cc_final: 0.8432 (p0) REVERT: A 1012 LEU cc_start: 0.9396 (mm) cc_final: 0.9065 (mm) REVERT: A 1015 TYR cc_start: 0.9011 (m-10) cc_final: 0.8738 (m-80) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0881 time to fit residues: 15.5890 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 : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3936 r_free = 0.3936 target = 0.079414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.067521 restraints weight = 43787.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.069197 restraints weight = 28688.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.070384 restraints weight = 20761.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.071254 restraints weight = 16103.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.071874 restraints weight = 13116.259| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7777 Z= 0.148 Angle : 0.695 8.311 10537 Z= 0.367 Chirality : 0.045 0.180 1224 Planarity : 0.005 0.053 1381 Dihedral : 5.394 20.567 1058 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.26), residues: 994 helix: 0.05 (0.21), residues: 580 sheet: -2.19 (0.95), residues: 33 loop : -2.27 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 496 TYR 0.018 0.001 TYR A 130 PHE 0.023 0.002 PHE A 918 TRP 0.003 0.001 TRP A 701 HIS 0.004 0.001 HIS A 500 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 7777) covalent geometry : angle 0.69512 (10537) hydrogen bonds : bond 0.03974 ( 388) hydrogen bonds : angle 5.59316 ( 1140) *********************** 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 118 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.7041 (ttt) cc_final: 0.6587 (tmm) REVERT: A 95 ASP cc_start: 0.8452 (t0) cc_final: 0.8202 (t0) REVERT: A 283 MET cc_start: 0.9044 (pmm) cc_final: 0.8692 (pmm) REVERT: A 461 ASP cc_start: 0.7601 (m-30) cc_final: 0.7344 (m-30) REVERT: A 675 LEU cc_start: 0.8149 (mm) cc_final: 0.7512 (mm) REVERT: A 776 MET cc_start: 0.8875 (mpp) cc_final: 0.8623 (mpp) REVERT: A 805 HIS cc_start: 0.7625 (m90) cc_final: 0.7274 (m90) REVERT: A 865 MET cc_start: 0.7713 (tpp) cc_final: 0.7194 (tpp) REVERT: A 1009 HIS cc_start: 0.8029 (m90) cc_final: 0.7785 (m90) REVERT: A 1011 ASP cc_start: 0.8908 (p0) cc_final: 0.8369 (p0) REVERT: A 1012 LEU cc_start: 0.9311 (mm) cc_final: 0.9038 (mm) REVERT: A 1015 TYR cc_start: 0.9029 (m-10) cc_final: 0.8720 (m-80) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.0801 time to fit residues: 13.4149 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 : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 0.0170 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 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 = 0.3957 r_free = 0.3957 target = 0.080440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.068690 restraints weight = 44819.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.070297 restraints weight = 29716.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.071510 restraints weight = 21644.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.072361 restraints weight = 16805.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.072944 restraints weight = 13730.174| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 7777 Z= 0.141 Angle : 0.706 10.123 10537 Z= 0.367 Chirality : 0.045 0.210 1224 Planarity : 0.005 0.053 1381 Dihedral : 5.343 20.515 1058 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.26), residues: 994 helix: 0.10 (0.21), residues: 581 sheet: -2.02 (0.96), residues: 33 loop : -2.26 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 496 TYR 0.017 0.001 TYR A 971 PHE 0.023 0.002 PHE A 290 TRP 0.003 0.001 TRP A 701 HIS 0.005 0.001 HIS A 905 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7777) covalent geometry : angle 0.70560 (10537) hydrogen bonds : bond 0.03847 ( 388) hydrogen bonds : angle 5.50113 ( 1140) *********************** 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 120 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.7011 (ttt) cc_final: 0.6555 (tmm) REVERT: A 95 ASP cc_start: 0.8466 (t0) cc_final: 0.8215 (t0) REVERT: A 461 ASP cc_start: 0.7664 (m-30) cc_final: 0.7401 (m-30) REVERT: A 805 HIS cc_start: 0.7743 (m90) cc_final: 0.7379 (m90) REVERT: A 865 MET cc_start: 0.7656 (tpp) cc_final: 0.7128 (tpp) REVERT: A 901 ASN cc_start: 0.8928 (p0) cc_final: 0.8698 (p0) REVERT: A 1009 HIS cc_start: 0.8115 (m90) cc_final: 0.7857 (m90) REVERT: A 1011 ASP cc_start: 0.9032 (p0) cc_final: 0.8434 (p0) REVERT: A 1012 LEU cc_start: 0.9324 (mm) cc_final: 0.9057 (mm) REVERT: A 1015 TYR cc_start: 0.9084 (m-10) cc_final: 0.8780 (m-80) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.0780 time to fit residues: 13.4043 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 : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 45 optimal weight: 0.0030 chunk 90 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 87 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3967 r_free = 0.3967 target = 0.080923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.069157 restraints weight = 44324.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.070788 restraints weight = 29610.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.071960 restraints weight = 21678.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.072792 restraints weight = 16948.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.073381 restraints weight = 13928.943| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2679 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= 0.140 Angle : 0.730 9.718 10537 Z= 0.374 Chirality : 0.045 0.209 1224 Planarity : 0.005 0.052 1381 Dihedral : 5.275 20.427 1058 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.26), residues: 994 helix: 0.07 (0.21), residues: 581 sheet: -1.87 (0.96), residues: 35 loop : -2.20 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 496 TYR 0.012 0.001 TYR A 130 PHE 0.022 0.002 PHE A 907 TRP 0.003 0.001 TRP A 701 HIS 0.004 0.001 HIS A 459 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7777) covalent geometry : angle 0.73040 (10537) hydrogen bonds : bond 0.03786 ( 388) hydrogen bonds : angle 5.49039 ( 1140) *********************** 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 116 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.6816 (ttt) cc_final: 0.6478 (tmm) REVERT: A 95 ASP cc_start: 0.8413 (t0) cc_final: 0.8168 (t0) REVERT: A 805 HIS cc_start: 0.7572 (m90) cc_final: 0.7339 (m90) REVERT: A 852 LEU cc_start: 0.8327 (pp) cc_final: 0.8068 (tt) REVERT: A 865 MET cc_start: 0.7558 (tpp) cc_final: 0.7095 (tpp) REVERT: A 901 ASN cc_start: 0.9020 (p0) cc_final: 0.8726 (p0) REVERT: A 1011 ASP cc_start: 0.9020 (p0) cc_final: 0.8433 (p0) REVERT: A 1012 LEU cc_start: 0.9331 (mm) cc_final: 0.9053 (mm) REVERT: A 1015 TYR cc_start: 0.9059 (m-10) cc_final: 0.8785 (m-80) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0830 time to fit residues: 13.6332 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 : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 26 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 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 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 = 0.3959 r_free = 0.3959 target = 0.080529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.068779 restraints weight = 44221.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.070411 restraints weight = 29300.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.071567 restraints weight = 21381.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.072406 restraints weight = 16702.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.072992 restraints weight = 13710.552| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7777 Z= 0.148 Angle : 0.734 9.816 10537 Z= 0.377 Chirality : 0.046 0.209 1224 Planarity : 0.005 0.053 1381 Dihedral : 5.303 20.947 1058 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.26), residues: 994 helix: 0.03 (0.21), residues: 582 sheet: -1.95 (0.96), residues: 33 loop : -2.21 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 595 TYR 0.012 0.001 TYR A 130 PHE 0.022 0.002 PHE A 907 TRP 0.003 0.001 TRP A 701 HIS 0.007 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7777) covalent geometry : angle 0.73399 (10537) hydrogen bonds : bond 0.03818 ( 388) hydrogen bonds : angle 5.52916 ( 1140) ********************** 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 116 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.6805 (ttt) cc_final: 0.6486 (tmm) REVERT: A 95 ASP cc_start: 0.8424 (t0) cc_final: 0.8188 (t0) REVERT: A 331 GLN cc_start: 0.7114 (mm-40) cc_final: 0.6410 (tm-30) REVERT: A 666 MET cc_start: 0.7944 (ppp) cc_final: 0.7688 (ppp) REVERT: A 776 MET cc_start: 0.8823 (mmm) cc_final: 0.8516 (mpp) REVERT: A 805 HIS cc_start: 0.7613 (m90) cc_final: 0.7290 (m90) REVERT: A 865 MET cc_start: 0.7564 (tpp) cc_final: 0.7100 (tpp) REVERT: A 901 ASN cc_start: 0.8995 (p0) cc_final: 0.8706 (p0) REVERT: A 1011 ASP cc_start: 0.9065 (p0) cc_final: 0.8458 (p0) REVERT: A 1012 LEU cc_start: 0.9349 (mm) cc_final: 0.9006 (mm) REVERT: A 1015 TYR cc_start: 0.9062 (m-10) cc_final: 0.8721 (m-80) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0713 time to fit residues: 12.0041 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 : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 87 optimal weight: 0.1980 chunk 48 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.081548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.069671 restraints weight = 43743.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.071339 restraints weight = 28689.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.072537 restraints weight = 20857.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.073379 restraints weight = 16205.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.074016 restraints weight = 13290.664| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 7777 Z= 0.138 Angle : 0.731 10.763 10537 Z= 0.373 Chirality : 0.045 0.201 1224 Planarity : 0.005 0.053 1381 Dihedral : 5.187 21.007 1058 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.26), residues: 994 helix: 0.09 (0.21), residues: 586 sheet: -1.81 (0.96), residues: 35 loop : -2.16 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 595 TYR 0.014 0.001 TYR A 872 PHE 0.021 0.002 PHE A 918 TRP 0.004 0.001 TRP A 701 HIS 0.008 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7777) covalent geometry : angle 0.73090 (10537) hydrogen bonds : bond 0.03782 ( 388) hydrogen bonds : angle 5.47394 ( 1140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1712.49 seconds wall clock time: 30 minutes 23.81 seconds (1823.81 seconds total)