Starting phenix.real_space_refine on Fri Mar 14 01:53:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fg2_31574/03_2025/7fg2_31574.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fg2_31574/03_2025/7fg2_31574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fg2_31574/03_2025/7fg2_31574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fg2_31574/03_2025/7fg2_31574.map" model { file = "/net/cci-nas-00/data/ceres_data/7fg2_31574/03_2025/7fg2_31574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fg2_31574/03_2025/7fg2_31574.cif" } resolution = 4.4 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= 0.002 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 41 5.16 5 C 5932 2.51 5 N 1574 2.21 5 O 1795 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9342 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8468 Classifications: {'peptide': 1086} Link IDs: {'PTRANS': 50, 'TRANS': 1035} Chain breaks: 2 Chain: "D" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 874 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Time building chain proxies: 5.98, per 1000 atoms: 0.64 Number of scatterers: 9342 At special positions: 0 Unit cell: (92.43, 139.356, 182.016, 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 41 16.00 O 1795 8.00 N 1574 7.00 C 5932 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.01 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.2 seconds 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 19 sheets defined 21.6% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.839A pdb=" N GLY A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.704A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.458A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.119A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 756 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 811 through 815 removed outlier: 4.060A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.627A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.965A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.221A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.766A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.245A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1034 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.605A pdb=" N ASP D 91 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR D 92 " --> pdb=" O PRO D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 92' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.847A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.850A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.561A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 227 removed outlier: 3.981A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 189 Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 379 through 380 removed outlier: 4.682A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 454 removed outlier: 4.365A pdb=" N ASN A 450 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR A 495 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU A 452 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN A 493 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 Processing sheet with id=AB2, first strand: chain 'A' and resid 643 through 645 removed outlier: 3.518A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 713 through 722 removed outlier: 6.882A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AB5, first strand: chain 'A' and resid 735 through 736 removed outlier: 3.548A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1076 through 1077 Processing sheet with id=AB7, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AB8, first strand: chain 'D' and resid 6 through 8 removed outlier: 4.263A pdb=" N CYS D 23 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL D 80 " --> pdb=" O CYS D 23 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 36 through 40 removed outlier: 8.124A pdb=" N TRP D 37 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL D 49 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 93 through 95 278 hydrogen bonds defined for protein. 741 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 3.08 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: 3002 1.34 - 1.46: 1876 1.46 - 1.58: 4622 1.58 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 9553 Sorted by residual: bond pdb=" CA TYR A 612 " pdb=" CB TYR A 612 " ideal model delta sigma weight residual 1.528 1.484 0.043 1.39e-02 5.18e+03 9.79e+00 bond pdb=" C ILE A 726 " pdb=" N LEU A 727 " ideal model delta sigma weight residual 1.331 1.291 0.040 1.36e-02 5.41e+03 8.50e+00 bond pdb=" CB VAL A 687 " pdb=" CG1 VAL A 687 " ideal model delta sigma weight residual 1.521 1.433 0.088 3.30e-02 9.18e+02 7.12e+00 bond pdb=" CA SER A 982 " pdb=" C SER A 982 " ideal model delta sigma weight residual 1.523 1.485 0.038 1.48e-02 4.57e+03 6.70e+00 bond pdb=" CB THR A 299 " pdb=" CG2 THR A 299 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.65e+00 ... (remaining 9548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 11989 1.97 - 3.93: 837 3.93 - 5.90: 129 5.90 - 7.86: 28 7.86 - 9.82: 9 Bond angle restraints: 12992 Sorted by residual: angle pdb=" N VAL A 483 " pdb=" CA VAL A 483 " pdb=" C VAL A 483 " ideal model delta sigma weight residual 113.71 106.29 7.42 9.50e-01 1.11e+00 6.10e+01 angle pdb=" N SER A 325 " pdb=" CA SER A 325 " pdb=" C SER A 325 " ideal model delta sigma weight residual 107.73 116.63 -8.90 1.34e+00 5.57e-01 4.41e+01 angle pdb=" C LEU A 176 " pdb=" N MET A 177 " pdb=" CA MET A 177 " ideal model delta sigma weight residual 121.54 131.36 -9.82 1.91e+00 2.74e-01 2.65e+01 angle pdb=" C MET A 177 " pdb=" N ASP A 178 " pdb=" CA ASP A 178 " ideal model delta sigma weight residual 121.54 131.32 -9.78 1.91e+00 2.74e-01 2.62e+01 angle pdb=" N SER A 591 " pdb=" CA SER A 591 " pdb=" CB SER A 591 " ideal model delta sigma weight residual 114.17 108.42 5.75 1.14e+00 7.69e-01 2.54e+01 ... (remaining 12987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5144 17.97 - 35.94: 418 35.94 - 53.92: 67 53.92 - 71.89: 17 71.89 - 89.86: 14 Dihedral angle restraints: 5660 sinusoidal: 2182 harmonic: 3478 Sorted by residual: dihedral pdb=" CA ASP A 178 " pdb=" C ASP A 178 " pdb=" N LEU A 179 " pdb=" CA LEU A 179 " ideal model delta harmonic sigma weight residual -180.00 -119.39 -60.61 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA SER A 591 " pdb=" C SER A 591 " pdb=" N PHE A 592 " pdb=" CA PHE A 592 " ideal model delta harmonic sigma weight residual 180.00 125.20 54.80 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" CA ALA A 623 " pdb=" C ALA A 623 " pdb=" N ILE A 624 " pdb=" CA ILE A 624 " ideal model delta harmonic sigma weight residual 180.00 -125.21 -54.79 0 5.00e+00 4.00e-02 1.20e+02 ... (remaining 5657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 959 0.043 - 0.086: 340 0.086 - 0.129: 132 0.129 - 0.173: 26 0.173 - 0.216: 8 Chirality restraints: 1465 Sorted by residual: chirality pdb=" CB THR A 274 " pdb=" CA THR A 274 " pdb=" OG1 THR A 274 " pdb=" CG2 THR A 274 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB THR A 827 " pdb=" CA THR A 827 " pdb=" OG1 THR A 827 " pdb=" CG2 THR A 827 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA VAL A 705 " pdb=" N VAL A 705 " pdb=" C VAL A 705 " pdb=" CB VAL A 705 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1462 not shown) Planarity restraints: 1689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 599 " -0.050 5.00e-02 4.00e+02 7.71e-02 9.51e+00 pdb=" N PRO A 600 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 600 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 600 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 714 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.41e+00 pdb=" N PRO A 715 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 715 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 715 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 321 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO A 322 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " -0.035 5.00e-02 4.00e+02 ... (remaining 1686 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 253 2.62 - 3.19: 9728 3.19 - 3.76: 14685 3.76 - 4.33: 20347 4.33 - 4.90: 31549 Nonbonded interactions: 76562 Sorted by model distance: nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.053 3.040 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.058 3.040 nonbonded pdb=" OD1 ASN A 709 " pdb=" N ASN A 710 " model vdw 2.058 3.120 nonbonded pdb=" OG1 THR A 478 " pdb=" OD1 ASN A 481 " model vdw 2.061 3.040 nonbonded pdb=" OG SER D 18 " pdb=" OD1 ASN D 85 " model vdw 2.091 3.040 ... (remaining 76557 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.610 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: 0.070 Set scattering table: 0.080 Process input model: 25.890 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 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 : 0.007 0.088 9553 Z= 0.451 Angle : 1.134 9.825 12992 Z= 0.679 Chirality : 0.053 0.216 1465 Planarity : 0.006 0.077 1689 Dihedral : 14.434 89.862 3405 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 32.64 Ramachandran Plot: Outliers : 0.42 % Allowed : 17.84 % Favored : 81.74 % Rotamer: Outliers : 0.19 % Allowed : 0.19 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.70 % 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: -3.95 (0.22), residues: 1194 helix: -0.70 (0.34), residues: 222 sheet: -2.12 (0.34), residues: 217 loop : -3.63 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A1102 HIS 0.006 0.002 HIS A1083 PHE 0.028 0.003 PHE A 797 TYR 0.027 0.003 TYR A 789 ARG 0.011 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.7650 (t) cc_final: 0.7359 (t) REVERT: A 137 ASN cc_start: 0.6800 (p0) cc_final: 0.6326 (p0) REVERT: A 220 PHE cc_start: 0.7007 (t80) cc_final: 0.6699 (t80) REVERT: A 223 LEU cc_start: 0.8221 (mp) cc_final: 0.8004 (mp) REVERT: A 350 VAL cc_start: 0.8770 (p) cc_final: 0.8000 (p) REVERT: A 400 PHE cc_start: 0.8231 (p90) cc_final: 0.7715 (p90) REVERT: A 559 PHE cc_start: 0.7741 (m-10) cc_final: 0.7463 (m-10) REVERT: A 738 CYS cc_start: 0.9078 (t) cc_final: 0.8693 (t) REVERT: A 818 ILE cc_start: 0.7786 (mt) cc_final: 0.6824 (mt) REVERT: A 823 PHE cc_start: 0.7910 (t80) cc_final: 0.7635 (t80) REVERT: A 900 MET cc_start: 0.7036 (mpp) cc_final: 0.6520 (mpp) REVERT: A 1010 GLN cc_start: 0.8808 (tp-100) cc_final: 0.8271 (tp-100) REVERT: D 71 ILE cc_start: 0.3741 (tp) cc_final: 0.3287 (tp) REVERT: D 84 MET cc_start: 0.5086 (pmm) cc_final: 0.4704 (pmm) outliers start: 2 outliers final: 0 residues processed: 222 average time/residue: 0.2214 time to fit residues: 68.9560 Evaluate side-chains 167 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.0770 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.0070 chunk 30 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 211 ASN A 343 ASN A 448 ASN A 606 ASN A 655 HIS A 777 ASN A 824 ASN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN A 935 GLN A1005 GLN D 83 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.181953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.152538 restraints weight = 26168.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.154586 restraints weight = 17615.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.156252 restraints weight = 13261.407| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9553 Z= 0.215 Angle : 0.765 10.968 12992 Z= 0.414 Chirality : 0.049 0.240 1465 Planarity : 0.006 0.065 1689 Dihedral : 7.302 66.218 1296 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.42 % Allowed : 13.40 % Favored : 86.18 % Rotamer: Outliers : 0.48 % Allowed : 5.02 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.44 % 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: -3.34 (0.23), residues: 1194 helix: 0.26 (0.35), residues: 220 sheet: -1.75 (0.36), residues: 195 loop : -3.34 (0.20), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS A 655 PHE 0.022 0.002 PHE A 592 TYR 0.020 0.002 TYR A 451 ARG 0.006 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 247 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8037 (pp30) cc_final: 0.7681 (pp30) REVERT: A 137 ASN cc_start: 0.5642 (p0) cc_final: 0.5297 (p0) REVERT: A 221 SER cc_start: 0.7572 (t) cc_final: 0.7347 (m) REVERT: A 274 THR cc_start: 0.8009 (t) cc_final: 0.7642 (t) REVERT: A 350 VAL cc_start: 0.8247 (p) cc_final: 0.7711 (p) REVERT: A 400 PHE cc_start: 0.7905 (p90) cc_final: 0.7556 (p90) REVERT: A 608 VAL cc_start: 0.5577 (p) cc_final: 0.5216 (p) REVERT: A 729 VAL cc_start: 0.8304 (t) cc_final: 0.8057 (p) REVERT: A 773 GLU cc_start: 0.7305 (tm-30) cc_final: 0.6750 (tm-30) REVERT: A 777 ASN cc_start: 0.8505 (m110) cc_final: 0.8200 (m110) REVERT: A 900 MET cc_start: 0.6492 (mpp) cc_final: 0.6245 (mpp) REVERT: A 933 LYS cc_start: 0.8825 (tttm) cc_final: 0.8307 (tttt) REVERT: A 1005 GLN cc_start: 0.8582 (tp40) cc_final: 0.8351 (tp40) REVERT: A 1010 GLN cc_start: 0.8277 (tp-100) cc_final: 0.7881 (tp40) REVERT: A 1027 THR cc_start: 0.8032 (m) cc_final: 0.7766 (m) REVERT: A 1028 LYS cc_start: 0.6135 (tptt) cc_final: 0.5922 (tptt) REVERT: A 1043 CYS cc_start: 0.3887 (m) cc_final: 0.3462 (m) REVERT: A 1049 LEU cc_start: 0.6483 (mt) cc_final: 0.6081 (mp) REVERT: A 1064 HIS cc_start: 0.6022 (m170) cc_final: 0.5584 (m170) REVERT: D 33 TYR cc_start: 0.5854 (m-80) cc_final: 0.5561 (m-80) outliers start: 5 outliers final: 0 residues processed: 248 average time/residue: 0.2478 time to fit residues: 87.4652 Evaluate side-chains 188 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 34 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 50 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN ** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.181927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.151759 restraints weight = 26318.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.154225 restraints weight = 16984.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.155977 restraints weight = 12240.329| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9553 Z= 0.201 Angle : 0.724 10.589 12992 Z= 0.389 Chirality : 0.047 0.178 1465 Planarity : 0.005 0.059 1689 Dihedral : 6.923 65.369 1296 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.42 % Allowed : 14.24 % Favored : 85.34 % Rotamer: Outliers : 0.29 % Allowed : 3.86 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.35 % 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: -3.18 (0.23), residues: 1194 helix: 0.28 (0.34), residues: 228 sheet: -1.76 (0.36), residues: 182 loop : -3.17 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.007 0.001 HIS A 655 PHE 0.023 0.002 PHE A 592 TYR 0.015 0.001 TYR A 451 ARG 0.006 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 222 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8043 (pp30) cc_final: 0.7747 (pp30) REVERT: A 274 THR cc_start: 0.7792 (t) cc_final: 0.7311 (t) REVERT: A 303 LEU cc_start: 0.8508 (tt) cc_final: 0.8303 (tt) REVERT: A 350 VAL cc_start: 0.8336 (p) cc_final: 0.7211 (p) REVERT: A 400 PHE cc_start: 0.7971 (p90) cc_final: 0.7578 (p90) REVERT: A 646 ARG cc_start: 0.7354 (mtp85) cc_final: 0.7089 (mpt180) REVERT: A 727 LEU cc_start: 0.8373 (mp) cc_final: 0.8127 (mp) REVERT: A 732 THR cc_start: 0.8721 (p) cc_final: 0.8424 (p) REVERT: A 738 CYS cc_start: 0.8368 (t) cc_final: 0.8107 (t) REVERT: A 773 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6614 (tm-30) REVERT: A 774 GLN cc_start: 0.8315 (mm-40) cc_final: 0.8043 (mm-40) REVERT: A 777 ASN cc_start: 0.8534 (m110) cc_final: 0.8044 (m110) REVERT: A 900 MET cc_start: 0.7142 (mpp) cc_final: 0.6753 (mpp) REVERT: A 985 ASP cc_start: 0.7752 (m-30) cc_final: 0.7447 (m-30) REVERT: A 1005 GLN cc_start: 0.8651 (tp40) cc_final: 0.8396 (tp40) REVERT: A 1010 GLN cc_start: 0.8448 (tp-100) cc_final: 0.7786 (tp-100) REVERT: A 1012 LEU cc_start: 0.8871 (mt) cc_final: 0.8557 (mt) REVERT: A 1031 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7077 (mt-10) REVERT: A 1052 PHE cc_start: 0.7877 (m-10) cc_final: 0.7490 (m-10) REVERT: A 1064 HIS cc_start: 0.6392 (m170) cc_final: 0.6110 (m170) REVERT: D 33 TYR cc_start: 0.6086 (m-80) cc_final: 0.5749 (m-80) REVERT: D 85 ASN cc_start: 0.6404 (m-40) cc_final: 0.5990 (p0) outliers start: 3 outliers final: 0 residues processed: 222 average time/residue: 0.2054 time to fit residues: 64.3671 Evaluate side-chains 181 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 48 optimal weight: 0.9990 chunk 76 optimal weight: 0.0870 chunk 3 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.181448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.151449 restraints weight = 26612.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.153866 restraints weight = 17070.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.155684 restraints weight = 12308.976| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9553 Z= 0.206 Angle : 0.689 9.416 12992 Z= 0.370 Chirality : 0.046 0.168 1465 Planarity : 0.005 0.056 1689 Dihedral : 6.674 65.664 1296 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.50 % Allowed : 13.15 % Favored : 86.35 % Rotamer: Outliers : 0.19 % Allowed : 3.96 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.23), residues: 1194 helix: 0.34 (0.34), residues: 232 sheet: -1.57 (0.36), residues: 194 loop : -3.06 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 37 HIS 0.008 0.001 HIS A 655 PHE 0.023 0.002 PHE A1075 TYR 0.015 0.001 TYR A 453 ARG 0.004 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8103 (pp30) cc_final: 0.7660 (pp30) REVERT: A 80 ASP cc_start: 0.8210 (p0) cc_final: 0.7941 (p0) REVERT: A 182 LYS cc_start: 0.6004 (mtmm) cc_final: 0.5361 (mmmt) REVERT: A 220 PHE cc_start: 0.7316 (t80) cc_final: 0.6941 (t80) REVERT: A 350 VAL cc_start: 0.8350 (p) cc_final: 0.7229 (p) REVERT: A 400 PHE cc_start: 0.7871 (p90) cc_final: 0.7413 (p90) REVERT: A 563 GLN cc_start: 0.7231 (pt0) cc_final: 0.6986 (pt0) REVERT: A 640 SER cc_start: 0.7593 (p) cc_final: 0.7145 (t) REVERT: A 646 ARG cc_start: 0.7377 (mtp85) cc_final: 0.7172 (tpt170) REVERT: A 773 GLU cc_start: 0.6964 (tm-30) cc_final: 0.6454 (tm-30) REVERT: A 777 ASN cc_start: 0.8483 (m110) cc_final: 0.8134 (m110) REVERT: A 858 LEU cc_start: 0.8564 (mt) cc_final: 0.8138 (mt) REVERT: A 859 THR cc_start: 0.8469 (t) cc_final: 0.8175 (m) REVERT: A 900 MET cc_start: 0.7085 (mpp) cc_final: 0.6647 (mpp) REVERT: A 985 ASP cc_start: 0.7695 (m-30) cc_final: 0.7354 (m-30) REVERT: A 995 ARG cc_start: 0.8558 (mtp-110) cc_final: 0.8329 (ttm110) REVERT: A 1002 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7459 (tm-30) REVERT: A 1005 GLN cc_start: 0.8697 (tp40) cc_final: 0.8426 (tp40) REVERT: A 1010 GLN cc_start: 0.8326 (tp-100) cc_final: 0.8079 (tp-100) REVERT: A 1028 LYS cc_start: 0.5879 (tptt) cc_final: 0.5431 (tttt) REVERT: A 1038 LYS cc_start: 0.5384 (mmmt) cc_final: 0.5054 (mmtt) REVERT: A 1075 PHE cc_start: 0.6708 (m-10) cc_final: 0.6194 (m-10) REVERT: D 33 TYR cc_start: 0.6122 (m-80) cc_final: 0.5800 (m-80) REVERT: D 85 ASN cc_start: 0.6355 (m-40) cc_final: 0.5837 (p0) outliers start: 2 outliers final: 0 residues processed: 223 average time/residue: 0.2064 time to fit residues: 64.9356 Evaluate side-chains 177 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 61 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 0.0040 chunk 98 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.184363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.153748 restraints weight = 26488.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.156263 restraints weight = 17040.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.158093 restraints weight = 12296.664| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9553 Z= 0.182 Angle : 0.676 8.510 12992 Z= 0.362 Chirality : 0.046 0.242 1465 Planarity : 0.005 0.052 1689 Dihedral : 6.530 65.328 1296 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.31 % Favored : 87.27 % Rotamer: Outliers : 0.10 % Allowed : 3.47 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.23), residues: 1194 helix: 0.78 (0.35), residues: 216 sheet: -1.45 (0.37), residues: 192 loop : -2.98 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 37 HIS 0.008 0.001 HIS A 655 PHE 0.020 0.001 PHE A 592 TYR 0.017 0.001 TYR D 98 ARG 0.010 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7786 (pp30) cc_final: 0.7269 (pp30) REVERT: A 80 ASP cc_start: 0.8221 (p0) cc_final: 0.7973 (p0) REVERT: A 182 LYS cc_start: 0.6443 (mtmm) cc_final: 0.5854 (mmmt) REVERT: A 350 VAL cc_start: 0.8358 (p) cc_final: 0.7179 (p) REVERT: A 400 PHE cc_start: 0.7831 (p90) cc_final: 0.7121 (p90) REVERT: A 613 GLN cc_start: 0.8248 (mt0) cc_final: 0.7719 (mp10) REVERT: A 640 SER cc_start: 0.7552 (p) cc_final: 0.7113 (t) REVERT: A 732 THR cc_start: 0.8670 (p) cc_final: 0.8187 (p) REVERT: A 747 THR cc_start: 0.7342 (m) cc_final: 0.6989 (p) REVERT: A 773 GLU cc_start: 0.6989 (tm-30) cc_final: 0.6448 (tm-30) REVERT: A 774 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8023 (mm-40) REVERT: A 777 ASN cc_start: 0.8415 (m110) cc_final: 0.8058 (m110) REVERT: A 804 GLN cc_start: 0.5756 (tp-100) cc_final: 0.5201 (mm-40) REVERT: A 900 MET cc_start: 0.6826 (mpp) cc_final: 0.6585 (mpp) REVERT: A 985 ASP cc_start: 0.7679 (m-30) cc_final: 0.7386 (m-30) REVERT: A 995 ARG cc_start: 0.8511 (mtp-110) cc_final: 0.8298 (ttm110) REVERT: A 1002 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7416 (tm-30) REVERT: A 1005 GLN cc_start: 0.8669 (tp40) cc_final: 0.8362 (tp40) REVERT: A 1010 GLN cc_start: 0.8353 (tp-100) cc_final: 0.8022 (tp40) REVERT: A 1049 LEU cc_start: 0.6800 (mt) cc_final: 0.6595 (mp) REVERT: A 1075 PHE cc_start: 0.6427 (m-10) cc_final: 0.4969 (m-10) REVERT: D 85 ASN cc_start: 0.6416 (m-40) cc_final: 0.5770 (p0) outliers start: 1 outliers final: 0 residues processed: 223 average time/residue: 0.2126 time to fit residues: 67.5371 Evaluate side-chains 176 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 31 optimal weight: 20.0000 chunk 79 optimal weight: 0.0570 chunk 19 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 0.0670 chunk 115 optimal weight: 0.0050 chunk 105 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 overall best weight: 0.7652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.184649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.155664 restraints weight = 26068.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.157545 restraints weight = 18712.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.157816 restraints weight = 13566.822| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9553 Z= 0.179 Angle : 0.661 9.114 12992 Z= 0.354 Chirality : 0.045 0.178 1465 Planarity : 0.004 0.049 1689 Dihedral : 6.334 60.463 1296 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.48 % Favored : 87.19 % Rotamer: Outliers : 0.19 % Allowed : 2.22 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.23), residues: 1194 helix: 0.76 (0.35), residues: 217 sheet: -1.37 (0.35), residues: 211 loop : -2.98 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 633 HIS 0.008 0.001 HIS A 655 PHE 0.025 0.001 PHE A 817 TYR 0.014 0.001 TYR A 453 ARG 0.010 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7758 (pp30) cc_final: 0.7269 (pp30) REVERT: A 80 ASP cc_start: 0.8274 (p0) cc_final: 0.8019 (p0) REVERT: A 182 LYS cc_start: 0.6530 (mtmm) cc_final: 0.6033 (mmmt) REVERT: A 220 PHE cc_start: 0.7326 (t80) cc_final: 0.6930 (t80) REVERT: A 350 VAL cc_start: 0.8448 (p) cc_final: 0.7273 (p) REVERT: A 400 PHE cc_start: 0.7786 (p90) cc_final: 0.7497 (p90) REVERT: A 613 GLN cc_start: 0.7771 (mt0) cc_final: 0.7349 (pt0) REVERT: A 640 SER cc_start: 0.7569 (p) cc_final: 0.7137 (t) REVERT: A 732 THR cc_start: 0.8648 (p) cc_final: 0.8403 (p) REVERT: A 747 THR cc_start: 0.7177 (m) cc_final: 0.6793 (p) REVERT: A 773 GLU cc_start: 0.7069 (tm-30) cc_final: 0.6505 (tm-30) REVERT: A 774 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8017 (mm-40) REVERT: A 777 ASN cc_start: 0.8402 (m110) cc_final: 0.8045 (m110) REVERT: A 858 LEU cc_start: 0.8634 (mt) cc_final: 0.8367 (mt) REVERT: A 985 ASP cc_start: 0.7859 (m-30) cc_final: 0.7455 (m-30) REVERT: A 995 ARG cc_start: 0.8584 (mtp-110) cc_final: 0.8332 (ttm110) REVERT: A 1002 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7431 (tm-30) REVERT: A 1005 GLN cc_start: 0.8774 (tp40) cc_final: 0.8400 (tp40) REVERT: A 1010 GLN cc_start: 0.8547 (tp-100) cc_final: 0.8130 (tp40) REVERT: A 1028 LYS cc_start: 0.6928 (tptp) cc_final: 0.5875 (ttmt) REVERT: A 1049 LEU cc_start: 0.6969 (mt) cc_final: 0.6745 (mp) REVERT: A 1075 PHE cc_start: 0.6091 (m-10) cc_final: 0.4665 (m-10) REVERT: D 33 TYR cc_start: 0.5062 (m-80) cc_final: 0.4578 (m-80) REVERT: D 85 ASN cc_start: 0.7112 (m-40) cc_final: 0.5736 (p0) outliers start: 2 outliers final: 0 residues processed: 218 average time/residue: 0.2752 time to fit residues: 85.3237 Evaluate side-chains 181 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 95 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 13 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.182258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.152936 restraints weight = 26975.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.154562 restraints weight = 17882.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.154787 restraints weight = 12876.463| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9553 Z= 0.215 Angle : 0.687 9.390 12992 Z= 0.368 Chirality : 0.046 0.168 1465 Planarity : 0.005 0.043 1689 Dihedral : 6.329 59.637 1296 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.32 % Favored : 86.35 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.23), residues: 1194 helix: 0.84 (0.36), residues: 217 sheet: -1.61 (0.35), residues: 214 loop : -2.94 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 633 HIS 0.008 0.001 HIS A 655 PHE 0.030 0.002 PHE A1121 TYR 0.019 0.002 TYR A 756 ARG 0.004 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7899 (pp30) cc_final: 0.7494 (pp30) REVERT: A 80 ASP cc_start: 0.8306 (p0) cc_final: 0.8094 (p0) REVERT: A 118 LEU cc_start: 0.7662 (tp) cc_final: 0.7443 (tp) REVERT: A 220 PHE cc_start: 0.7593 (t80) cc_final: 0.7201 (t80) REVERT: A 350 VAL cc_start: 0.8565 (p) cc_final: 0.7473 (p) REVERT: A 400 PHE cc_start: 0.7931 (p90) cc_final: 0.7461 (p90) REVERT: A 613 GLN cc_start: 0.7863 (mt0) cc_final: 0.7408 (pt0) REVERT: A 640 SER cc_start: 0.7592 (p) cc_final: 0.7102 (t) REVERT: A 732 THR cc_start: 0.8685 (p) cc_final: 0.8425 (p) REVERT: A 747 THR cc_start: 0.7433 (m) cc_final: 0.7034 (p) REVERT: A 773 GLU cc_start: 0.7020 (tm-30) cc_final: 0.6599 (tm-30) REVERT: A 774 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7858 (mm110) REVERT: A 777 ASN cc_start: 0.8522 (m110) cc_final: 0.8082 (m110) REVERT: A 985 ASP cc_start: 0.7755 (m-30) cc_final: 0.7419 (m-30) REVERT: A 1002 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7235 (tm-30) REVERT: A 1005 GLN cc_start: 0.8778 (tp40) cc_final: 0.8436 (tp40) REVERT: D 33 TYR cc_start: 0.4885 (m-80) cc_final: 0.4531 (m-80) REVERT: D 85 ASN cc_start: 0.7314 (m-40) cc_final: 0.5860 (p0) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1999 time to fit residues: 59.7806 Evaluate side-chains 165 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 77 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 64 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS A 926 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.184750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.155519 restraints weight = 26605.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.157513 restraints weight = 17116.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.159175 restraints weight = 11674.743| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9553 Z= 0.180 Angle : 0.662 9.327 12992 Z= 0.354 Chirality : 0.046 0.160 1465 Planarity : 0.004 0.042 1689 Dihedral : 6.114 57.230 1296 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.15 % Favored : 86.52 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.23), residues: 1194 helix: 0.77 (0.36), residues: 218 sheet: -1.24 (0.35), residues: 218 loop : -2.96 (0.20), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 107 HIS 0.008 0.001 HIS A 655 PHE 0.022 0.001 PHE A1121 TYR 0.014 0.001 TYR A 453 ARG 0.004 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7884 (pp30) cc_final: 0.7544 (pp30) REVERT: A 80 ASP cc_start: 0.8201 (p0) cc_final: 0.7972 (p0) REVERT: A 220 PHE cc_start: 0.7613 (t80) cc_final: 0.7385 (t80) REVERT: A 350 VAL cc_start: 0.8457 (p) cc_final: 0.7263 (p) REVERT: A 374 PHE cc_start: 0.5582 (p90) cc_final: 0.4850 (p90) REVERT: A 400 PHE cc_start: 0.7701 (p90) cc_final: 0.7448 (p90) REVERT: A 640 SER cc_start: 0.7443 (p) cc_final: 0.7022 (t) REVERT: A 732 THR cc_start: 0.8596 (p) cc_final: 0.8293 (p) REVERT: A 747 THR cc_start: 0.7255 (m) cc_final: 0.6938 (p) REVERT: A 773 GLU cc_start: 0.7060 (tm-30) cc_final: 0.6444 (tm-30) REVERT: A 774 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7863 (mm110) REVERT: A 777 ASN cc_start: 0.8398 (m110) cc_final: 0.7994 (m110) REVERT: A 804 GLN cc_start: 0.6580 (mm-40) cc_final: 0.5152 (tp-100) REVERT: A 935 GLN cc_start: 0.7463 (tp-100) cc_final: 0.6069 (tp-100) REVERT: A 985 ASP cc_start: 0.7569 (m-30) cc_final: 0.7322 (m-30) REVERT: A 1002 GLN cc_start: 0.7916 (tm-30) cc_final: 0.7370 (tm-30) REVERT: A 1005 GLN cc_start: 0.8585 (tp40) cc_final: 0.8382 (tp40) REVERT: A 1028 LYS cc_start: 0.6777 (tptp) cc_final: 0.6000 (ttpt) REVERT: A 1049 LEU cc_start: 0.6942 (mt) cc_final: 0.6727 (mp) REVERT: D 85 ASN cc_start: 0.7691 (m-40) cc_final: 0.5837 (p0) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.2546 time to fit residues: 74.4129 Evaluate side-chains 163 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 0.0000 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 77 optimal weight: 0.0770 chunk 3 optimal weight: 0.0870 chunk 24 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS A 955 ASN A1106 GLN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.186348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.155913 restraints weight = 26008.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.158580 restraints weight = 16453.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.160393 restraints weight = 11687.579| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9553 Z= 0.168 Angle : 0.664 9.486 12992 Z= 0.354 Chirality : 0.046 0.229 1465 Planarity : 0.004 0.042 1689 Dihedral : 5.952 55.256 1296 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.48 % Favored : 87.19 % Rotamer: Outliers : 0.10 % Allowed : 1.16 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.23), residues: 1194 helix: 0.67 (0.36), residues: 217 sheet: -1.10 (0.36), residues: 210 loop : -2.85 (0.20), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 107 HIS 0.007 0.001 HIS A 655 PHE 0.024 0.001 PHE A 592 TYR 0.014 0.001 TYR A 248 ARG 0.006 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7860 (pp30) cc_final: 0.7570 (pp30) REVERT: A 80 ASP cc_start: 0.8083 (p0) cc_final: 0.7859 (p0) REVERT: A 291 CYS cc_start: 0.7519 (p) cc_final: 0.7237 (p) REVERT: A 350 VAL cc_start: 0.8309 (p) cc_final: 0.7065 (p) REVERT: A 374 PHE cc_start: 0.5404 (p90) cc_final: 0.4695 (p90) REVERT: A 400 PHE cc_start: 0.7641 (p90) cc_final: 0.7404 (p90) REVERT: A 627 ASP cc_start: 0.7050 (p0) cc_final: 0.6688 (p0) REVERT: A 747 THR cc_start: 0.7338 (m) cc_final: 0.7044 (p) REVERT: A 773 GLU cc_start: 0.7065 (tm-30) cc_final: 0.5955 (tm-30) REVERT: A 774 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8119 (mm-40) REVERT: A 777 ASN cc_start: 0.8429 (m110) cc_final: 0.7800 (m110) REVERT: A 1002 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7552 (tm-30) REVERT: A 1005 GLN cc_start: 0.8644 (tp40) cc_final: 0.8300 (tp40) REVERT: A 1049 LEU cc_start: 0.6951 (mt) cc_final: 0.6680 (mp) REVERT: A 1132 ILE cc_start: 0.5901 (mm) cc_final: 0.5377 (mm) REVERT: D 85 ASN cc_start: 0.7334 (m-40) cc_final: 0.5438 (p0) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.2068 time to fit residues: 62.3084 Evaluate side-chains 169 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 43 optimal weight: 10.0000 chunk 19 optimal weight: 0.4980 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.183921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.153292 restraints weight = 26568.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.155995 restraints weight = 16616.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.157908 restraints weight = 11693.351| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9553 Z= 0.206 Angle : 0.701 9.872 12992 Z= 0.372 Chirality : 0.047 0.216 1465 Planarity : 0.005 0.049 1689 Dihedral : 6.069 56.864 1296 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.57 % Favored : 86.10 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.23), residues: 1194 helix: 0.71 (0.36), residues: 217 sheet: -1.48 (0.35), residues: 221 loop : -2.80 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 107 HIS 0.009 0.001 HIS A 655 PHE 0.032 0.002 PHE A1121 TYR 0.015 0.001 TYR A 660 ARG 0.009 0.001 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7979 (pp30) cc_final: 0.7476 (pp30) REVERT: A 80 ASP cc_start: 0.8160 (p0) cc_final: 0.7952 (p0) REVERT: A 220 PHE cc_start: 0.7603 (t80) cc_final: 0.7376 (t80) REVERT: A 265 TYR cc_start: 0.7265 (p90) cc_final: 0.7015 (p90) REVERT: A 350 VAL cc_start: 0.8460 (p) cc_final: 0.7296 (p) REVERT: A 374 PHE cc_start: 0.5572 (p90) cc_final: 0.5018 (p90) REVERT: A 400 PHE cc_start: 0.7699 (p90) cc_final: 0.7468 (p90) REVERT: A 729 VAL cc_start: 0.8223 (t) cc_final: 0.7983 (p) REVERT: A 747 THR cc_start: 0.7288 (m) cc_final: 0.7003 (p) REVERT: A 773 GLU cc_start: 0.6835 (tm-30) cc_final: 0.6559 (tm-30) REVERT: A 777 ASN cc_start: 0.8063 (m110) cc_final: 0.7846 (m110) REVERT: A 985 ASP cc_start: 0.7750 (m-30) cc_final: 0.7493 (m-30) REVERT: A 986 LYS cc_start: 0.8265 (mmmt) cc_final: 0.7919 (mmtm) REVERT: A 995 ARG cc_start: 0.8518 (mtp-110) cc_final: 0.8307 (ttm110) REVERT: A 1002 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7429 (tm-30) REVERT: A 1005 GLN cc_start: 0.8668 (tp40) cc_final: 0.8359 (tp40) REVERT: D 33 TYR cc_start: 0.4724 (m-80) cc_final: 0.4450 (m-80) REVERT: D 85 ASN cc_start: 0.7400 (m-40) cc_final: 0.5367 (p0) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2592 time to fit residues: 71.5730 Evaluate side-chains 162 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 108 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.180081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.149289 restraints weight = 27130.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.151755 restraints weight = 17492.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.153559 restraints weight = 12607.265| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9553 Z= 0.294 Angle : 0.776 9.966 12992 Z= 0.411 Chirality : 0.049 0.208 1465 Planarity : 0.005 0.050 1689 Dihedral : 6.605 55.935 1296 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.34 % Allowed : 14.99 % Favored : 84.67 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.23), residues: 1194 helix: 0.63 (0.37), residues: 211 sheet: -1.64 (0.36), residues: 207 loop : -2.80 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 353 HIS 0.005 0.002 HIS A 655 PHE 0.039 0.002 PHE A1121 TYR 0.021 0.002 TYR A 904 ARG 0.007 0.001 ARG A 685 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3280.05 seconds wall clock time: 60 minutes 0.77 seconds (3600.77 seconds total)