Starting phenix.real_space_refine on Tue Sep 24 09:56:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptx_13642/09_2024/7ptx_13642.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptx_13642/09_2024/7ptx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptx_13642/09_2024/7ptx_13642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptx_13642/09_2024/7ptx_13642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptx_13642/09_2024/7ptx_13642.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptx_13642/09_2024/7ptx_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-5461/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: 4.87, per 1000 atoms: 0.64 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: 1.87 Conformation dependent library (CDL) restraints added in 1.0 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: 0.86 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: 2.15 Time building geometry restraints manager: 2.17 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: 3.920 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.700 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.890 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.901 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: 0.1946 time to fit residues: 32.1768 Evaluate side-chains 90 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 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 fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.7391 (tpt) cc_final: 0.6792 (tpp) REVERT: A 283 MET cc_start: 0.9212 (pmm) cc_final: 0.8745 (pmm) REVERT: A 666 MET cc_start: 0.8215 (ppp) cc_final: 0.7617 (ppp) REVERT: A 1011 ASP cc_start: 0.8814 (p0) cc_final: 0.8231 (p0) REVERT: A 1012 LEU cc_start: 0.9223 (mm) cc_final: 0.8928 (mm) outliers start: 2 outliers final: 0 residues processed: 124 average time/residue: 0.1807 time to fit residues: 31.2165 Evaluate side-chains 91 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7777 Z= 0.228 Angle : 0.675 6.019 10537 Z= 0.361 Chirality : 0.044 0.155 1224 Planarity : 0.005 0.054 1381 Dihedral : 5.565 21.391 1058 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 0.37 % Allowed : 6.95 % Favored : 92.68 % 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: -1.65 (0.26), residues: 994 helix: -0.15 (0.21), residues: 586 sheet: -3.24 (0.77), residues: 35 loop : -2.36 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 701 HIS 0.006 0.002 HIS A 772 PHE 0.019 0.002 PHE A 290 TYR 0.014 0.002 TYR A 130 ARG 0.009 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 123 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.7643 (ttt) cc_final: 0.7362 (tmm) REVERT: A 277 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7471 (t0) REVERT: A 283 MET cc_start: 0.9203 (pmm) cc_final: 0.8709 (pmm) REVERT: A 494 MET cc_start: 0.6828 (mpp) cc_final: 0.6592 (mpp) REVERT: A 666 MET cc_start: 0.8220 (ppp) cc_final: 0.7954 (ppp) REVERT: A 776 MET cc_start: 0.8855 (mpp) cc_final: 0.8631 (mpp) REVERT: A 865 MET cc_start: 0.7571 (tpp) cc_final: 0.7107 (tpp) outliers start: 3 outliers final: 0 residues processed: 122 average time/residue: 0.1749 time to fit residues: 30.0792 Evaluate side-chains 87 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 91 optimal weight: 0.0070 chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- 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 277 ASN ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1877 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= 0.198 Angle : 0.664 7.064 10537 Z= 0.349 Chirality : 0.044 0.155 1224 Planarity : 0.005 0.065 1381 Dihedral : 5.479 21.295 1058 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 0.37 % Allowed : 5.71 % Favored : 93.92 % 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: -1.48 (0.26), residues: 994 helix: -0.01 (0.21), residues: 585 sheet: -3.02 (0.81), residues: 35 loop : -2.32 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 384 HIS 0.004 0.001 HIS A 772 PHE 0.020 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 fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8582 (tp) REVERT: A 666 MET cc_start: 0.8127 (ppp) cc_final: 0.7666 (ppp) REVERT: A 675 LEU cc_start: 0.7930 (mm) cc_final: 0.7582 (mm) REVERT: A 717 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7325 (pm20) REVERT: A 1009 HIS cc_start: 0.7727 (m90) cc_final: 0.7513 (m90) REVERT: A 1011 ASP cc_start: 0.8906 (p0) cc_final: 0.8222 (p0) REVERT: A 1012 LEU cc_start: 0.9292 (mm) cc_final: 0.8887 (mm) REVERT: A 1015 TYR cc_start: 0.8819 (m-80) cc_final: 0.8588 (m-80) outliers start: 3 outliers final: 0 residues processed: 127 average time/residue: 0.1943 time to fit residues: 33.6452 Evaluate side-chains 95 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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: 0.6980 chunk 71 optimal weight: 0.0770 chunk 39 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 86 optimal weight: 0.0980 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN A 921 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2119 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 : 0.666 7.794 10537 Z= 0.350 Chirality : 0.044 0.159 1224 Planarity : 0.005 0.053 1381 Dihedral : 5.329 20.827 1058 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 0.25 % Allowed : 4.34 % Favored : 95.41 % 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: -1.38 (0.26), residues: 994 helix: 0.07 (0.21), residues: 580 sheet: -2.73 (0.85), residues: 35 loop : -2.27 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 701 HIS 0.004 0.001 HIS A 459 PHE 0.020 0.001 PHE A 290 TYR 0.021 0.002 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 fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8598 (tp) REVERT: A 461 ASP cc_start: 0.7648 (m-30) cc_final: 0.7361 (m-30) REVERT: A 675 LEU cc_start: 0.7894 (mm) cc_final: 0.7452 (mm) REVERT: A 805 HIS cc_start: 0.7245 (m90) cc_final: 0.6927 (m90) REVERT: A 865 MET cc_start: 0.7531 (tpp) cc_final: 0.7054 (tpp) REVERT: A 934 LYS cc_start: 0.7725 (tttm) cc_final: 0.6518 (tttm) REVERT: A 1011 ASP cc_start: 0.8841 (p0) cc_final: 0.8133 (p0) REVERT: A 1012 LEU cc_start: 0.9286 (mm) cc_final: 0.8884 (mm) outliers start: 2 outliers final: 0 residues processed: 125 average time/residue: 0.1828 time to fit residues: 32.0401 Evaluate side-chains 97 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 96 optimal weight: 0.0270 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 10 optimal weight: 0.0010 overall best weight: 0.4844 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7777 Z= 0.189 Angle : 0.669 8.090 10537 Z= 0.349 Chirality : 0.044 0.154 1224 Planarity : 0.005 0.052 1381 Dihedral : 5.274 20.894 1058 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: -2.24 (0.94), residues: 33 loop : -2.28 (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 0.019 0.001 PHE A 290 TYR 0.011 0.001 TYR A 130 ARG 0.005 0.000 ARG A 496 *********************** 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 fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ASP cc_start: 0.8159 (t0) cc_final: 0.7956 (t0) REVERT: A 461 ASP cc_start: 0.7610 (m-30) cc_final: 0.7324 (m-30) REVERT: A 675 LEU cc_start: 0.7960 (mm) cc_final: 0.7391 (mm) REVERT: A 851 MET cc_start: 0.8694 (mtm) cc_final: 0.8477 (mtt) REVERT: A 852 LEU cc_start: 0.8484 (pp) cc_final: 0.8053 (tt) REVERT: A 865 MET cc_start: 0.7510 (tpp) cc_final: 0.7050 (tpp) REVERT: A 918 PHE cc_start: 0.8496 (m-10) cc_final: 0.8199 (m-10) REVERT: A 1011 ASP cc_start: 0.8631 (p0) cc_final: 0.8185 (p0) REVERT: A 1012 LEU cc_start: 0.9264 (mm) cc_final: 0.8943 (mm) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2013 time to fit residues: 34.9666 Evaluate side-chains 96 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 96 optimal weight: 0.0030 chunk 60 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7777 Z= 0.201 Angle : 0.694 8.527 10537 Z= 0.365 Chirality : 0.044 0.176 1224 Planarity : 0.005 0.053 1381 Dihedral : 5.262 20.442 1058 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % 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: -1.33 (0.26), residues: 994 helix: 0.07 (0.21), residues: 582 sheet: -2.07 (0.96), residues: 33 loop : -2.27 (0.31), residues: 379 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 0.029 0.001 PHE A 918 TYR 0.038 0.002 TYR A1015 ARG 0.008 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 120 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.7369 (ttt) cc_final: 0.6797 (tmm) REVERT: A 91 SER cc_start: 0.8491 (m) cc_final: 0.8168 (t) REVERT: A 95 ASP cc_start: 0.8199 (t0) cc_final: 0.7979 (t0) REVERT: A 283 MET cc_start: 0.9130 (pmm) cc_final: 0.8834 (pmm) REVERT: A 461 ASP cc_start: 0.7587 (m-30) cc_final: 0.7303 (m-30) REVERT: A 865 MET cc_start: 0.7525 (tpp) cc_final: 0.7092 (tpp) REVERT: A 901 ASN cc_start: 0.8701 (p0) cc_final: 0.8480 (p0) REVERT: A 1011 ASP cc_start: 0.8612 (p0) cc_final: 0.8133 (p0) REVERT: A 1012 LEU cc_start: 0.9272 (mm) cc_final: 0.8948 (mm) REVERT: A 1015 TYR cc_start: 0.8790 (m-80) cc_final: 0.8400 (m-80) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1700 time to fit residues: 29.4101 Evaluate side-chains 98 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 0.0770 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2610 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= 0.209 Angle : 0.713 10.530 10537 Z= 0.369 Chirality : 0.046 0.203 1224 Planarity : 0.004 0.053 1381 Dihedral : 5.328 20.307 1058 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: -1.36 (0.26), residues: 994 helix: 0.02 (0.21), residues: 583 sheet: -2.00 (0.96), 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 500 PHE 0.022 0.002 PHE A 290 TYR 0.031 0.002 TYR A1015 ARG 0.005 0.000 ARG A 344 *********************** 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 118 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.7516 (ttt) cc_final: 0.6936 (tmm) REVERT: A 91 SER cc_start: 0.8484 (m) cc_final: 0.8169 (t) REVERT: A 95 ASP cc_start: 0.8235 (t0) cc_final: 0.8013 (t0) REVERT: A 283 MET cc_start: 0.9191 (pmm) cc_final: 0.8958 (pmm) REVERT: A 331 GLN cc_start: 0.7155 (mm-40) cc_final: 0.6311 (tm-30) REVERT: A 461 ASP cc_start: 0.7586 (m-30) cc_final: 0.7305 (m-30) REVERT: A 675 LEU cc_start: 0.8023 (mm) cc_final: 0.7506 (mm) REVERT: A 865 MET cc_start: 0.7459 (tpp) cc_final: 0.7033 (tpp) REVERT: A 901 ASN cc_start: 0.8794 (p0) cc_final: 0.8561 (p0) REVERT: A 1011 ASP cc_start: 0.8655 (p0) cc_final: 0.8103 (p0) REVERT: A 1012 LEU cc_start: 0.9248 (mm) cc_final: 0.8924 (mm) REVERT: A 1015 TYR cc_start: 0.8794 (m-80) cc_final: 0.8500 (m-80) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1656 time to fit residues: 27.9138 Evaluate side-chains 98 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 7777 Z= 0.268 Angle : 0.748 8.521 10537 Z= 0.392 Chirality : 0.047 0.201 1224 Planarity : 0.005 0.053 1381 Dihedral : 5.549 20.973 1058 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % 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: -1.61 (0.26), residues: 994 helix: -0.18 (0.21), residues: 584 sheet: -1.89 (0.95), residues: 31 loop : -2.36 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 701 HIS 0.005 0.001 HIS A 267 PHE 0.023 0.002 PHE A 907 TYR 0.030 0.002 TYR A1015 ARG 0.007 0.001 ARG A 344 *********************** 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 fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.7604 (ttt) cc_final: 0.7067 (tmm) REVERT: A 91 SER cc_start: 0.8549 (m) cc_final: 0.8242 (t) REVERT: A 283 MET cc_start: 0.9272 (pmm) cc_final: 0.8734 (pmm) REVERT: A 331 GLN cc_start: 0.7170 (mm-40) cc_final: 0.6275 (tm-30) REVERT: A 339 SER cc_start: 0.9013 (m) cc_final: 0.8811 (m) REVERT: A 461 ASP cc_start: 0.7554 (m-30) cc_final: 0.7288 (m-30) REVERT: A 666 MET cc_start: 0.7976 (ppp) cc_final: 0.7746 (ppp) REVERT: A 772 HIS cc_start: 0.8401 (m90) cc_final: 0.8172 (m90) REVERT: A 865 MET cc_start: 0.7491 (tpp) cc_final: 0.7030 (tpp) REVERT: A 1009 HIS cc_start: 0.7427 (m90) cc_final: 0.7057 (m90) REVERT: A 1011 ASP cc_start: 0.8728 (p0) cc_final: 0.8101 (p0) REVERT: A 1015 TYR cc_start: 0.8838 (m-80) cc_final: 0.8589 (m-80) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1817 time to fit residues: 29.7116 Evaluate side-chains 91 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 63 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 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 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 7777 Z= 0.227 Angle : 0.749 10.211 10537 Z= 0.384 Chirality : 0.046 0.217 1224 Planarity : 0.005 0.053 1381 Dihedral : 5.484 21.637 1058 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: -1.53 (0.26), residues: 994 helix: -0.14 (0.21), residues: 581 sheet: -2.06 (0.93), residues: 35 loop : -2.26 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 701 HIS 0.005 0.001 HIS A 459 PHE 0.023 0.002 PHE A 290 TYR 0.028 0.002 TYR A1015 ARG 0.004 0.000 ARG A 344 ********************** 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 114 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.7572 (ttt) cc_final: 0.6936 (tmm) REVERT: A 91 SER cc_start: 0.8558 (m) cc_final: 0.7962 (m) REVERT: A 331 GLN cc_start: 0.7145 (mm-40) cc_final: 0.6317 (tm-30) REVERT: A 339 SER cc_start: 0.9028 (m) cc_final: 0.8807 (m) REVERT: A 461 ASP cc_start: 0.7504 (m-30) cc_final: 0.7236 (m-30) REVERT: A 865 MET cc_start: 0.7442 (tpp) cc_final: 0.6999 (tpp) REVERT: A 901 ASN cc_start: 0.8787 (p0) cc_final: 0.8536 (p0) REVERT: A 1011 ASP cc_start: 0.8833 (p0) cc_final: 0.8170 (p0) REVERT: A 1012 LEU cc_start: 0.9312 (mm) cc_final: 0.8887 (mm) REVERT: A 1015 TYR cc_start: 0.8796 (m-80) cc_final: 0.8509 (m-80) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2344 time to fit residues: 39.3547 Evaluate side-chains 92 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 79 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 4 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 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 = 0.3919 r_free = 0.3919 target = 0.078790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.067013 restraints weight = 43752.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.068564 restraints weight = 29222.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.069684 restraints weight = 21466.168| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 7777 Z= 0.253 Angle : 0.762 9.553 10537 Z= 0.393 Chirality : 0.048 0.219 1224 Planarity : 0.005 0.053 1381 Dihedral : 5.594 21.454 1058 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -1.59 (0.26), residues: 994 helix: -0.16 (0.21), residues: 575 sheet: -1.79 (0.96), residues: 31 loop : -2.34 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 701 HIS 0.008 0.002 HIS A 213 PHE 0.026 0.002 PHE A 907 TYR 0.028 0.002 TYR A1015 ARG 0.005 0.001 ARG A 613 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1932.54 seconds wall clock time: 35 minutes 22.20 seconds (2122.20 seconds total)