Starting phenix.real_space_refine on Sat Dec 28 15:21:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qfw_13950/12_2024/7qfw_13950.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qfw_13950/12_2024/7qfw_13950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qfw_13950/12_2024/7qfw_13950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qfw_13950/12_2024/7qfw_13950.map" model { file = "/net/cci-nas-00/data/ceres_data/7qfw_13950/12_2024/7qfw_13950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qfw_13950/12_2024/7qfw_13950.cif" } resolution = 3.86 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= 0.001 sd= 0.025 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: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 32 5.16 5 C 5395 2.51 5 N 1492 2.21 5 O 1782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8765 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 6643 Classifications: {'peptide': 823} Link IDs: {'PTRANS': 20, 'TRANS': 802} Chain breaks: 3 Chain: "B" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 810 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain breaks: 1 Chain: "C" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 672 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "D" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 640 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Time building chain proxies: 5.50, per 1000 atoms: 0.63 Number of scatterers: 8765 At special positions: 0 Unit cell: (79.04, 111.28, 132.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 64 15.00 O 1782 8.00 N 1492 7.00 C 5395 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 927.5 milliseconds 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1786 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 73.9% alpha, 0.0% beta 30 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'A' and resid 8 through 24 removed outlier: 4.032A pdb=" N PHE A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 49 removed outlier: 3.811A pdb=" N ALA A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 64 Processing helix chain 'A' and resid 72 through 98 removed outlier: 3.737A pdb=" N ASP A 76 " --> pdb=" O GLU A 72 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 123 removed outlier: 3.629A pdb=" N ARG A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 removed outlier: 3.780A pdb=" N ARG A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 removed outlier: 4.112A pdb=" N GLY A 149 " --> pdb=" O MET A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 Processing helix chain 'A' and resid 171 through 184 removed outlier: 3.658A pdb=" N ARG A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.949A pdb=" N THR A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 228 removed outlier: 3.540A pdb=" N ALA A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 242 Processing helix chain 'A' and resid 243 through 246 Processing helix chain 'A' and resid 248 through 258 removed outlier: 3.571A pdb=" N ARG A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 265 through 268 removed outlier: 3.699A pdb=" N PHE A 268 " --> pdb=" O ARG A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 272 through 285 removed outlier: 3.734A pdb=" N GLN A 278 " --> pdb=" O HIS A 274 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLU A 281 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 301 removed outlier: 3.508A pdb=" N ARG A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 347 through 351 removed outlier: 3.791A pdb=" N ILE A 350 " --> pdb=" O PRO A 347 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TRP A 351 " --> pdb=" O GLU A 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 347 through 351' Processing helix chain 'A' and resid 355 through 372 Processing helix chain 'A' and resid 374 through 380 Processing helix chain 'A' and resid 384 through 401 Processing helix chain 'A' and resid 414 through 430 Processing helix chain 'A' and resid 436 through 451 Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 474 through 500 removed outlier: 3.681A pdb=" N PHE A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 493 " --> pdb=" O ILE A 489 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 587 removed outlier: 3.502A pdb=" N ILE A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 607 through 612 removed outlier: 3.655A pdb=" N ARG A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 631 Processing helix chain 'A' and resid 633 through 650 removed outlier: 3.837A pdb=" N ALA A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N TYR A 642 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE A 643 " --> pdb=" O ASP A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 671 Processing helix chain 'A' and resid 682 through 695 Processing helix chain 'A' and resid 699 through 716 Processing helix chain 'A' and resid 722 through 734 Processing helix chain 'A' and resid 740 through 751 removed outlier: 3.659A pdb=" N ILE A 751 " --> pdb=" O PHE A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 758 removed outlier: 3.760A pdb=" N SER A 757 " --> pdb=" O VAL A 753 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS A 758 " --> pdb=" O TYR A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 785 removed outlier: 4.404A pdb=" N ALA A 770 " --> pdb=" O SER A 766 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASP A 771 " --> pdb=" O ARG A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 810 Processing helix chain 'A' and resid 820 through 825 removed outlier: 3.711A pdb=" N LYS A 823 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A 825 " --> pdb=" O THR A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 839 Processing helix chain 'A' and resid 840 through 842 No H-bonds generated for 'chain 'A' and resid 840 through 842' Processing helix chain 'A' and resid 846 through 853 Processing helix chain 'A' and resid 854 through 858 removed outlier: 3.886A pdb=" N ALA A 857 " --> pdb=" O ASN A 854 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 858 " --> pdb=" O ILE A 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 854 through 858' Processing helix chain 'A' and resid 866 through 883 removed outlier: 4.207A pdb=" N LEU A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 883 " --> pdb=" O ILE A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 908 removed outlier: 4.311A pdb=" N ALA A 892 " --> pdb=" O VAL A 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 398 Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 through 401' Processing helix chain 'B' and resid 470 through 474 Processing helix chain 'B' and resid 486 through 490 removed outlier: 3.519A pdb=" N ASN B 489 " --> pdb=" O PRO B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 511 421 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 3.38 Time building geometry restraints manager: 2.64 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: 2296 1.34 - 1.45: 1885 1.45 - 1.57: 4689 1.57 - 1.69: 126 1.69 - 1.81: 50 Bond restraints: 9046 Sorted by residual: bond pdb=" CA ASN A 672 " pdb=" C ASN A 672 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.40e-02 5.10e+03 9.69e+00 bond pdb=" N GLN A 99 " pdb=" CA GLN A 99 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.60e+00 bond pdb=" N ASP A 319 " pdb=" CA ASP A 319 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.91e+00 bond pdb=" C ILE A 751 " pdb=" N PRO A 752 " ideal model delta sigma weight residual 1.335 1.356 -0.022 1.28e-02 6.10e+03 2.92e+00 bond pdb=" CA GLY A 149 " pdb=" C GLY A 149 " ideal model delta sigma weight residual 1.530 1.513 0.018 1.04e-02 9.25e+03 2.87e+00 ... (remaining 9041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 12299 3.09 - 6.19: 181 6.19 - 9.28: 10 9.28 - 12.37: 3 12.37 - 15.47: 1 Bond angle restraints: 12494 Sorted by residual: angle pdb=" C LYS A 98 " pdb=" N GLN A 99 " pdb=" CA GLN A 99 " ideal model delta sigma weight residual 121.54 130.88 -9.34 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C3' DT D 9 " pdb=" O3' DT D 9 " pdb=" P DT D 10 " ideal model delta sigma weight residual 120.20 127.45 -7.25 1.50e+00 4.44e-01 2.34e+01 angle pdb=" CA LEU A 307 " pdb=" CB LEU A 307 " pdb=" CG LEU A 307 " ideal model delta sigma weight residual 116.30 131.77 -15.47 3.50e+00 8.16e-02 1.95e+01 angle pdb=" C LEU A 318 " pdb=" N ASP A 319 " pdb=" CA ASP A 319 " ideal model delta sigma weight residual 121.54 129.70 -8.16 1.91e+00 2.74e-01 1.82e+01 angle pdb=" CA ARG B 411 " pdb=" CB ARG B 411 " pdb=" CG ARG B 411 " ideal model delta sigma weight residual 114.10 121.76 -7.66 2.00e+00 2.50e-01 1.47e+01 ... (remaining 12489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.37: 4651 27.37 - 54.74: 670 54.74 - 82.11: 81 82.11 - 109.48: 6 109.48 - 136.84: 2 Dihedral angle restraints: 5410 sinusoidal: 2689 harmonic: 2721 Sorted by residual: dihedral pdb=" CA LYS A 98 " pdb=" C LYS A 98 " pdb=" N GLN A 99 " pdb=" CA GLN A 99 " ideal model delta harmonic sigma weight residual -180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ASP B 462 " pdb=" C ASP B 462 " pdb=" N PHE B 463 " pdb=" CA PHE B 463 " ideal model delta harmonic sigma weight residual 180.00 -154.39 -25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLN A 818 " pdb=" C GLN A 818 " pdb=" N THR A 819 " pdb=" CA THR A 819 " ideal model delta harmonic sigma weight residual -180.00 -156.27 -23.73 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 5407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 953 0.044 - 0.088: 354 0.088 - 0.132: 95 0.132 - 0.175: 28 0.175 - 0.219: 8 Chirality restraints: 1438 Sorted by residual: chirality pdb=" P DT D 10 " pdb=" OP1 DT D 10 " pdb=" OP2 DT D 10 " pdb=" O5' DT D 10 " both_signs ideal model delta sigma weight residual True 2.35 -2.56 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASP A 319 " pdb=" N ASP A 319 " pdb=" C ASP A 319 " pdb=" CB ASP A 319 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" C1' DA C 16 " pdb=" O4' DA C 16 " pdb=" C2' DA C 16 " pdb=" N9 DA C 16 " both_signs ideal model delta sigma weight residual False 2.42 2.23 0.19 2.00e-01 2.50e+01 9.39e-01 ... (remaining 1435 not shown) Planarity restraints: 1373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 66 " -0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO A 67 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 67 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 67 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 608 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.05e+00 pdb=" N PRO A 609 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 609 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 609 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 798 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.41e+00 pdb=" N PRO A 799 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 799 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 799 " 0.038 5.00e-02 4.00e+02 ... (remaining 1370 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2303 2.80 - 3.33: 8063 3.33 - 3.85: 15330 3.85 - 4.38: 17579 4.38 - 4.90: 27470 Nonbonded interactions: 70745 Sorted by model distance: nonbonded pdb=" O PRO A 383 " pdb=" OH TYR A 432 " model vdw 2.276 3.040 nonbonded pdb=" O THR A 826 " pdb=" OG1 THR A 830 " model vdw 2.298 3.040 nonbonded pdb=" O SER A 862 " pdb=" OG SER A 862 " model vdw 2.329 3.040 nonbonded pdb=" O GLU A 430 " pdb=" OG SER A 470 " model vdw 2.337 3.040 nonbonded pdb=" O THR A 727 " pdb=" OG SER A 731 " model vdw 2.346 3.040 ... (remaining 70740 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.740 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: 32.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 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 : 0.006 0.065 9046 Z= 0.379 Angle : 0.984 15.467 12494 Z= 0.579 Chirality : 0.052 0.219 1438 Planarity : 0.008 0.079 1373 Dihedral : 22.546 136.844 3624 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.36 % Allowed : 6.92 % Favored : 92.72 % 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: -4.68 (0.20), residues: 905 helix: -2.90 (0.14), residues: 630 sheet: None (None), residues: 0 loop : -3.13 (0.29), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 780 HIS 0.008 0.001 HIS A 394 PHE 0.023 0.002 PHE A 354 TYR 0.018 0.002 TYR B 496 ARG 0.005 0.001 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7665 (mttm) cc_final: 0.7382 (mmtp) REVERT: A 13 ILE cc_start: 0.7989 (mm) cc_final: 0.7588 (mt) REVERT: A 39 LYS cc_start: 0.7811 (tptt) cc_final: 0.7554 (tptt) REVERT: A 47 GLU cc_start: 0.6706 (tm-30) cc_final: 0.6286 (tm-30) REVERT: A 72 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7153 (tm-30) REVERT: A 107 GLU cc_start: 0.8005 (mp0) cc_final: 0.7695 (mm-30) REVERT: A 136 ARG cc_start: 0.7191 (mmt-90) cc_final: 0.6952 (mmt-90) REVERT: A 266 LYS cc_start: 0.7948 (mmmm) cc_final: 0.7733 (mtmm) REVERT: A 285 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6817 (mm-30) REVERT: A 384 GLU cc_start: 0.6657 (tm-30) cc_final: 0.6238 (tm-30) REVERT: A 421 ILE cc_start: 0.6590 (mt) cc_final: 0.6382 (mm) REVERT: A 471 LEU cc_start: 0.7946 (tp) cc_final: 0.7728 (tp) REVERT: A 641 MET cc_start: 0.7488 (tpp) cc_final: 0.7086 (tpt) REVERT: A 644 LEU cc_start: 0.8161 (mt) cc_final: 0.7891 (mp) REVERT: A 648 VAL cc_start: 0.7331 (p) cc_final: 0.7103 (p) REVERT: A 695 LYS cc_start: 0.7067 (mttt) cc_final: 0.6836 (mttp) REVERT: A 705 ILE cc_start: 0.8051 (pt) cc_final: 0.7699 (mt) REVERT: A 808 PHE cc_start: 0.7944 (t80) cc_final: 0.7727 (t80) REVERT: A 837 LYS cc_start: 0.7459 (mttm) cc_final: 0.7235 (ttmm) REVERT: A 841 GLN cc_start: 0.7527 (mt0) cc_final: 0.7208 (tt0) REVERT: A 895 LYS cc_start: 0.7385 (tttt) cc_final: 0.7183 (ttpt) REVERT: B 408 TRP cc_start: 0.6047 (p-90) cc_final: 0.4806 (p-90) outliers start: 3 outliers final: 0 residues processed: 195 average time/residue: 0.2619 time to fit residues: 66.5628 Evaluate side-chains 176 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 31 HIS A 34 HIS A 42 GLN A 71 ASN A 121 HIS A 372 ASN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS A 402 HIS A 613 ASN A 697 ASN A 758 HIS A 884 ASN B 401 ASN B 495 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9046 Z= 0.214 Angle : 0.628 8.496 12494 Z= 0.353 Chirality : 0.040 0.187 1438 Planarity : 0.005 0.058 1373 Dihedral : 24.699 137.471 1749 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.55 % Allowed : 12.65 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.24), residues: 905 helix: -1.08 (0.19), residues: 621 sheet: None (None), residues: 0 loop : -2.85 (0.29), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 408 HIS 0.007 0.001 HIS A 687 PHE 0.015 0.001 PHE A 354 TYR 0.015 0.001 TYR A 657 ARG 0.007 0.001 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7680 (mttm) cc_final: 0.7364 (mmtp) REVERT: A 13 ILE cc_start: 0.8013 (mm) cc_final: 0.7629 (mt) REVERT: A 19 GLU cc_start: 0.7164 (tt0) cc_final: 0.6914 (tt0) REVERT: A 31 HIS cc_start: 0.6875 (OUTLIER) cc_final: 0.6636 (m-70) REVERT: A 39 LYS cc_start: 0.7814 (tptt) cc_final: 0.7461 (tptt) REVERT: A 72 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7462 (tm-30) REVERT: A 107 GLU cc_start: 0.7971 (mp0) cc_final: 0.7689 (mm-30) REVERT: A 227 MET cc_start: 0.7328 (ttm) cc_final: 0.7114 (ttm) REVERT: A 288 GLU cc_start: 0.6677 (tm-30) cc_final: 0.6466 (tm-30) REVERT: A 333 LEU cc_start: 0.8106 (mt) cc_final: 0.7759 (tp) REVERT: A 421 ILE cc_start: 0.6548 (mt) cc_final: 0.6345 (mm) REVERT: A 692 LYS cc_start: 0.7839 (mmmt) cc_final: 0.7539 (mmmt) REVERT: A 695 LYS cc_start: 0.7031 (mttt) cc_final: 0.6789 (mttp) REVERT: A 753 VAL cc_start: 0.8014 (p) cc_final: 0.7698 (t) REVERT: A 767 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.7448 (mtm-85) REVERT: A 841 GLN cc_start: 0.7576 (mt0) cc_final: 0.7319 (tt0) REVERT: A 895 LYS cc_start: 0.7512 (tttt) cc_final: 0.7250 (ttpt) REVERT: B 391 MET cc_start: 0.6325 (OUTLIER) cc_final: 0.5899 (mmt) REVERT: B 492 ASN cc_start: 0.8098 (t0) cc_final: 0.7650 (m-40) outliers start: 13 outliers final: 5 residues processed: 189 average time/residue: 0.2640 time to fit residues: 65.7743 Evaluate side-chains 173 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 166 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 73 optimal weight: 0.0000 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9046 Z= 0.213 Angle : 0.619 7.097 12494 Z= 0.345 Chirality : 0.040 0.190 1438 Planarity : 0.005 0.057 1373 Dihedral : 24.486 139.665 1749 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.39 % Allowed : 15.75 % Favored : 81.86 % 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: 905 helix: -0.44 (0.20), residues: 629 sheet: None (None), residues: 0 loop : -2.71 (0.30), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 780 HIS 0.009 0.001 HIS A 31 PHE 0.023 0.001 PHE A 808 TYR 0.014 0.001 TYR A 657 ARG 0.010 0.001 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7670 (mttm) cc_final: 0.7429 (mmtp) REVERT: A 13 ILE cc_start: 0.7972 (mm) cc_final: 0.7596 (mt) REVERT: A 19 GLU cc_start: 0.7171 (tt0) cc_final: 0.6921 (tt0) REVERT: A 39 LYS cc_start: 0.7821 (tptt) cc_final: 0.7550 (tptt) REVERT: A 72 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7519 (tm-30) REVERT: A 107 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7692 (mm-30) REVERT: A 291 VAL cc_start: 0.7523 (m) cc_final: 0.7057 (p) REVERT: A 333 LEU cc_start: 0.8083 (mt) cc_final: 0.7756 (tp) REVERT: A 384 GLU cc_start: 0.6808 (tm-30) cc_final: 0.6154 (tm-30) REVERT: A 641 MET cc_start: 0.7177 (tpt) cc_final: 0.6833 (tpt) REVERT: A 689 ILE cc_start: 0.7676 (mt) cc_final: 0.7449 (mt) REVERT: A 692 LYS cc_start: 0.7925 (mmmt) cc_final: 0.7611 (mmmt) REVERT: A 808 PHE cc_start: 0.7986 (t80) cc_final: 0.7626 (t80) REVERT: A 841 GLN cc_start: 0.7575 (mt0) cc_final: 0.7337 (tt0) REVERT: A 852 ILE cc_start: 0.7898 (mm) cc_final: 0.7691 (mm) REVERT: B 391 MET cc_start: 0.6254 (OUTLIER) cc_final: 0.5969 (mmt) REVERT: B 408 TRP cc_start: 0.5621 (p-90) cc_final: 0.4490 (p-90) REVERT: B 492 ASN cc_start: 0.8063 (t0) cc_final: 0.7684 (m-40) outliers start: 20 outliers final: 10 residues processed: 174 average time/residue: 0.2430 time to fit residues: 56.2642 Evaluate side-chains 169 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9046 Z= 0.240 Angle : 0.623 6.879 12494 Z= 0.346 Chirality : 0.041 0.186 1438 Planarity : 0.005 0.064 1373 Dihedral : 24.383 142.395 1749 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.98 % Allowed : 17.30 % Favored : 79.71 % 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: -1.52 (0.26), residues: 905 helix: -0.25 (0.20), residues: 635 sheet: None (None), residues: 0 loop : -2.74 (0.30), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 408 HIS 0.005 0.001 HIS A 121 PHE 0.013 0.001 PHE A 808 TYR 0.015 0.001 TYR A 657 ARG 0.010 0.001 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7638 (mttm) cc_final: 0.7208 (mttm) REVERT: A 13 ILE cc_start: 0.7996 (mm) cc_final: 0.7628 (mt) REVERT: A 19 GLU cc_start: 0.7190 (tt0) cc_final: 0.6969 (tt0) REVERT: A 39 LYS cc_start: 0.7863 (tptt) cc_final: 0.7638 (tptt) REVERT: A 107 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7691 (mm-30) REVERT: A 333 LEU cc_start: 0.8100 (mt) cc_final: 0.7727 (tp) REVERT: A 353 ASP cc_start: 0.6707 (t0) cc_final: 0.6498 (t0) REVERT: A 384 GLU cc_start: 0.7011 (tm-30) cc_final: 0.6592 (tm-30) REVERT: A 399 ARG cc_start: 0.6818 (tpt90) cc_final: 0.6577 (tpt-90) REVERT: A 431 ARG cc_start: 0.5237 (mtp180) cc_final: 0.4552 (mtp180) REVERT: A 443 MET cc_start: 0.7813 (tpp) cc_final: 0.7353 (tpt) REVERT: A 689 ILE cc_start: 0.7708 (mt) cc_final: 0.7467 (mt) REVERT: A 692 LYS cc_start: 0.7947 (mmmt) cc_final: 0.7656 (mmmt) REVERT: A 852 ILE cc_start: 0.8050 (mm) cc_final: 0.7818 (mm) REVERT: B 391 MET cc_start: 0.6158 (OUTLIER) cc_final: 0.5849 (mmt) REVERT: B 492 ASN cc_start: 0.8081 (t0) cc_final: 0.7717 (m-40) outliers start: 25 outliers final: 15 residues processed: 174 average time/residue: 0.2472 time to fit residues: 57.2266 Evaluate side-chains 173 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 520 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9046 Z= 0.238 Angle : 0.619 7.694 12494 Z= 0.343 Chirality : 0.040 0.183 1438 Planarity : 0.005 0.064 1373 Dihedral : 24.278 144.635 1749 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.98 % Allowed : 18.97 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.27), residues: 905 helix: -0.10 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.62 (0.31), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 351 HIS 0.018 0.001 HIS A 391 PHE 0.023 0.001 PHE A 808 TYR 0.013 0.001 TYR A 657 ARG 0.011 0.001 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.7963 (mm) cc_final: 0.7601 (mt) REVERT: A 19 GLU cc_start: 0.7184 (tt0) cc_final: 0.6965 (tt0) REVERT: A 107 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7701 (mm-30) REVERT: A 333 LEU cc_start: 0.8057 (mt) cc_final: 0.7730 (tp) REVERT: A 384 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6633 (tm-30) REVERT: A 399 ARG cc_start: 0.6852 (tpt90) cc_final: 0.6589 (tpt-90) REVERT: A 431 ARG cc_start: 0.5225 (mtp180) cc_final: 0.4597 (mtp180) REVERT: A 443 MET cc_start: 0.7801 (tpp) cc_final: 0.7337 (tpt) REVERT: A 493 ASP cc_start: 0.6653 (t0) cc_final: 0.6442 (t0) REVERT: A 584 TYR cc_start: 0.6982 (m-80) cc_final: 0.6722 (m-80) REVERT: A 641 MET cc_start: 0.6982 (tpt) cc_final: 0.6716 (tpt) REVERT: A 692 LYS cc_start: 0.7945 (mmmt) cc_final: 0.7661 (mmmt) REVERT: A 852 ILE cc_start: 0.8018 (mm) cc_final: 0.7738 (mm) REVERT: A 869 LEU cc_start: 0.7516 (mt) cc_final: 0.7220 (mt) REVERT: A 873 LEU cc_start: 0.7702 (mt) cc_final: 0.7491 (mm) REVERT: B 391 MET cc_start: 0.6061 (OUTLIER) cc_final: 0.5789 (mmt) REVERT: B 492 ASN cc_start: 0.8073 (t0) cc_final: 0.7677 (m-40) outliers start: 25 outliers final: 18 residues processed: 173 average time/residue: 0.2455 time to fit residues: 56.6154 Evaluate side-chains 179 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 520 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 chunk 93 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9046 Z= 0.214 Angle : 0.605 8.211 12494 Z= 0.335 Chirality : 0.040 0.169 1438 Planarity : 0.004 0.046 1373 Dihedral : 24.171 145.976 1749 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.74 % Allowed : 20.29 % Favored : 76.97 % 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: -1.08 (0.27), residues: 905 helix: 0.08 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -2.55 (0.32), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 780 HIS 0.005 0.001 HIS A 391 PHE 0.015 0.001 PHE A 808 TYR 0.014 0.001 TYR A 657 ARG 0.010 0.000 ARG A 910 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7618 (mttm) cc_final: 0.7215 (mttm) REVERT: A 13 ILE cc_start: 0.7971 (mm) cc_final: 0.7606 (mt) REVERT: A 107 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: A 252 ARG cc_start: 0.7021 (mtm110) cc_final: 0.6606 (mtm180) REVERT: A 291 VAL cc_start: 0.7468 (OUTLIER) cc_final: 0.6392 (m) REVERT: A 333 LEU cc_start: 0.8008 (mt) cc_final: 0.7660 (tp) REVERT: A 399 ARG cc_start: 0.6808 (tpt90) cc_final: 0.6442 (tpt-90) REVERT: A 431 ARG cc_start: 0.5058 (mtp180) cc_final: 0.4364 (mtp180) REVERT: A 443 MET cc_start: 0.7676 (tpp) cc_final: 0.7280 (tpt) REVERT: A 493 ASP cc_start: 0.6664 (t0) cc_final: 0.6421 (t0) REVERT: A 692 LYS cc_start: 0.7935 (mmmt) cc_final: 0.7642 (mmmt) REVERT: A 852 ILE cc_start: 0.7882 (mm) cc_final: 0.7671 (mm) REVERT: A 869 LEU cc_start: 0.7556 (mt) cc_final: 0.7236 (mt) REVERT: A 875 TYR cc_start: 0.7459 (m-80) cc_final: 0.7238 (m-80) REVERT: B 492 ASN cc_start: 0.8005 (t0) cc_final: 0.7623 (m-40) outliers start: 23 outliers final: 18 residues processed: 174 average time/residue: 0.2491 time to fit residues: 57.4095 Evaluate side-chains 179 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 520 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9046 Z= 0.232 Angle : 0.626 8.910 12494 Z= 0.344 Chirality : 0.040 0.143 1438 Planarity : 0.004 0.048 1373 Dihedral : 24.120 146.265 1749 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.86 % Allowed : 21.24 % Favored : 75.89 % 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: -1.08 (0.27), residues: 905 helix: 0.06 (0.21), residues: 641 sheet: None (None), residues: 0 loop : -2.56 (0.31), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 780 HIS 0.005 0.001 HIS A 391 PHE 0.009 0.001 PHE A 85 TYR 0.015 0.001 TYR A 657 ARG 0.011 0.000 ARG A 910 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7623 (mttm) cc_final: 0.7213 (mttm) REVERT: A 13 ILE cc_start: 0.7972 (mm) cc_final: 0.7612 (mt) REVERT: A 72 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7635 (tm-30) REVERT: A 107 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7686 (mm-30) REVERT: A 227 MET cc_start: 0.7585 (ttm) cc_final: 0.7351 (ttm) REVERT: A 288 GLU cc_start: 0.6440 (pm20) cc_final: 0.6160 (pm20) REVERT: A 291 VAL cc_start: 0.7259 (OUTLIER) cc_final: 0.7003 (m) REVERT: A 333 LEU cc_start: 0.8058 (mt) cc_final: 0.7712 (tp) REVERT: A 384 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6864 (tm-30) REVERT: A 399 ARG cc_start: 0.6837 (tpt90) cc_final: 0.6400 (tpt-90) REVERT: A 431 ARG cc_start: 0.4991 (mtp180) cc_final: 0.4241 (mtp180) REVERT: A 443 MET cc_start: 0.7753 (tpp) cc_final: 0.7290 (tpt) REVERT: A 493 ASP cc_start: 0.6604 (t0) cc_final: 0.6403 (t0) REVERT: A 689 ILE cc_start: 0.7640 (mt) cc_final: 0.7353 (mp) REVERT: A 692 LYS cc_start: 0.7949 (mmmt) cc_final: 0.7660 (mmmt) REVERT: A 852 ILE cc_start: 0.7898 (mm) cc_final: 0.7687 (mm) REVERT: A 869 LEU cc_start: 0.7489 (mt) cc_final: 0.7227 (mt) REVERT: A 875 TYR cc_start: 0.7481 (m-80) cc_final: 0.7258 (m-80) REVERT: B 391 MET cc_start: 0.6265 (mmp) cc_final: 0.5764 (mmt) REVERT: B 492 ASN cc_start: 0.7980 (t0) cc_final: 0.7620 (m-40) outliers start: 24 outliers final: 15 residues processed: 175 average time/residue: 0.2455 time to fit residues: 57.1557 Evaluate side-chains 178 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 520 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 73 optimal weight: 0.0010 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9046 Z= 0.224 Angle : 0.628 8.744 12494 Z= 0.343 Chirality : 0.040 0.149 1438 Planarity : 0.004 0.051 1373 Dihedral : 24.090 142.225 1749 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.74 % Allowed : 22.43 % Favored : 74.82 % 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: -1.00 (0.27), residues: 905 helix: 0.11 (0.21), residues: 641 sheet: None (None), residues: 0 loop : -2.50 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 351 HIS 0.010 0.001 HIS A 391 PHE 0.009 0.001 PHE A 808 TYR 0.015 0.001 TYR A 657 ARG 0.012 0.000 ARG A 910 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7606 (mttm) cc_final: 0.7208 (mttm) REVERT: A 13 ILE cc_start: 0.7976 (mm) cc_final: 0.7627 (mt) REVERT: A 107 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: A 185 PHE cc_start: 0.7134 (m-80) cc_final: 0.6729 (m-10) REVERT: A 190 GLN cc_start: 0.7904 (mp10) cc_final: 0.7703 (mp10) REVERT: A 227 MET cc_start: 0.7577 (ttm) cc_final: 0.7352 (ttm) REVERT: A 291 VAL cc_start: 0.7352 (OUTLIER) cc_final: 0.6560 (m) REVERT: A 333 LEU cc_start: 0.8007 (mt) cc_final: 0.7705 (tt) REVERT: A 431 ARG cc_start: 0.4973 (mtp180) cc_final: 0.4179 (mtp180) REVERT: A 443 MET cc_start: 0.7740 (tpp) cc_final: 0.7255 (tpt) REVERT: A 493 ASP cc_start: 0.6618 (t0) cc_final: 0.6395 (t0) REVERT: A 641 MET cc_start: 0.7126 (tpt) cc_final: 0.6866 (tpp) REVERT: A 689 ILE cc_start: 0.7661 (mt) cc_final: 0.7444 (mp) REVERT: A 692 LYS cc_start: 0.7937 (mmmt) cc_final: 0.7655 (mmmt) REVERT: A 852 ILE cc_start: 0.7881 (mm) cc_final: 0.7671 (mm) REVERT: A 869 LEU cc_start: 0.7300 (mt) cc_final: 0.7092 (mt) REVERT: A 875 TYR cc_start: 0.7469 (m-80) cc_final: 0.7262 (m-80) REVERT: B 391 MET cc_start: 0.6208 (mmp) cc_final: 0.5770 (mmt) outliers start: 23 outliers final: 16 residues processed: 170 average time/residue: 0.2327 time to fit residues: 52.5752 Evaluate side-chains 177 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 520 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.6980 chunk 89 optimal weight: 0.0970 chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9046 Z= 0.221 Angle : 0.640 10.475 12494 Z= 0.345 Chirality : 0.040 0.263 1438 Planarity : 0.004 0.053 1373 Dihedral : 24.055 137.515 1749 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.03 % Allowed : 23.03 % Favored : 74.94 % 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: -0.88 (0.27), residues: 905 helix: 0.22 (0.21), residues: 635 sheet: None (None), residues: 0 loop : -2.44 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 351 HIS 0.009 0.001 HIS A 391 PHE 0.011 0.001 PHE A 808 TYR 0.014 0.001 TYR A 657 ARG 0.012 0.000 ARG A 910 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7620 (mttm) cc_final: 0.7219 (mttm) REVERT: A 13 ILE cc_start: 0.7986 (mm) cc_final: 0.7624 (mt) REVERT: A 72 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7563 (tm-30) REVERT: A 107 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7612 (mm-30) REVERT: A 185 PHE cc_start: 0.7089 (m-80) cc_final: 0.6726 (m-10) REVERT: A 190 GLN cc_start: 0.7953 (mp10) cc_final: 0.7741 (mp10) REVERT: A 227 MET cc_start: 0.7583 (ttm) cc_final: 0.7337 (ttm) REVERT: A 333 LEU cc_start: 0.7976 (mt) cc_final: 0.7663 (tp) REVERT: A 431 ARG cc_start: 0.4967 (mtp180) cc_final: 0.4191 (mtp180) REVERT: A 443 MET cc_start: 0.7732 (tpp) cc_final: 0.7273 (tpt) REVERT: A 493 ASP cc_start: 0.6618 (t0) cc_final: 0.6395 (t0) REVERT: A 641 MET cc_start: 0.6990 (tpt) cc_final: 0.6739 (tpt) REVERT: A 648 VAL cc_start: 0.7248 (p) cc_final: 0.7041 (p) REVERT: A 692 LYS cc_start: 0.7932 (mmmt) cc_final: 0.7648 (mmmt) REVERT: A 852 ILE cc_start: 0.7882 (mm) cc_final: 0.7650 (mm) REVERT: A 875 TYR cc_start: 0.7456 (m-80) cc_final: 0.7255 (m-80) REVERT: B 391 MET cc_start: 0.6213 (mmp) cc_final: 0.5784 (mmt) outliers start: 17 outliers final: 15 residues processed: 166 average time/residue: 0.2516 time to fit residues: 55.8112 Evaluate side-chains 170 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9046 Z= 0.228 Angle : 0.653 10.410 12494 Z= 0.352 Chirality : 0.041 0.326 1438 Planarity : 0.004 0.055 1373 Dihedral : 24.043 136.240 1749 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.15 % Allowed : 22.67 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.84 (0.27), residues: 905 helix: 0.25 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -2.45 (0.32), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 351 HIS 0.007 0.001 HIS A 121 PHE 0.010 0.001 PHE A 354 TYR 0.015 0.001 TYR A 657 ARG 0.013 0.001 ARG A 910 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7621 (mttm) cc_final: 0.7217 (mttm) REVERT: A 13 ILE cc_start: 0.7973 (mm) cc_final: 0.7613 (mt) REVERT: A 72 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7568 (tm-30) REVERT: A 107 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7614 (mm-30) REVERT: A 185 PHE cc_start: 0.7060 (m-80) cc_final: 0.6706 (m-10) REVERT: A 190 GLN cc_start: 0.7965 (mp10) cc_final: 0.7763 (mp10) REVERT: A 227 MET cc_start: 0.7608 (ttm) cc_final: 0.7355 (ttm) REVERT: A 333 LEU cc_start: 0.7991 (mt) cc_final: 0.7672 (tp) REVERT: A 399 ARG cc_start: 0.6792 (tpt90) cc_final: 0.6437 (tpt-90) REVERT: A 431 ARG cc_start: 0.5101 (mtp180) cc_final: 0.4250 (mtp180) REVERT: A 443 MET cc_start: 0.7731 (tpp) cc_final: 0.7266 (tpt) REVERT: A 493 ASP cc_start: 0.6614 (t0) cc_final: 0.6401 (t0) REVERT: A 641 MET cc_start: 0.6950 (tpt) cc_final: 0.6663 (tpt) REVERT: A 689 ILE cc_start: 0.7650 (mt) cc_final: 0.7376 (mp) REVERT: A 692 LYS cc_start: 0.7927 (mmmt) cc_final: 0.7647 (mmmt) REVERT: A 852 ILE cc_start: 0.7887 (mm) cc_final: 0.7669 (mm) REVERT: A 869 LEU cc_start: 0.7484 (mm) cc_final: 0.7018 (mt) REVERT: B 391 MET cc_start: 0.6165 (mmp) cc_final: 0.5743 (mmt) outliers start: 18 outliers final: 16 residues processed: 167 average time/residue: 0.2508 time to fit residues: 55.8198 Evaluate side-chains 174 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 0.3980 chunk 70 optimal weight: 0.3980 chunk 11 optimal weight: 0.0970 chunk 21 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.165448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.141610 restraints weight = 12374.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.145314 restraints weight = 6878.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.147823 restraints weight = 4365.271| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9046 Z= 0.201 Angle : 0.638 11.104 12494 Z= 0.343 Chirality : 0.040 0.311 1438 Planarity : 0.004 0.056 1373 Dihedral : 23.981 133.095 1749 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.15 % Allowed : 23.03 % Favored : 74.82 % 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: -0.73 (0.27), residues: 905 helix: 0.36 (0.21), residues: 637 sheet: None (None), residues: 0 loop : -2.50 (0.31), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 780 HIS 0.007 0.001 HIS A 121 PHE 0.009 0.001 PHE A 362 TYR 0.014 0.001 TYR A 657 ARG 0.013 0.000 ARG A 910 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2031.16 seconds wall clock time: 38 minutes 19.27 seconds (2299.27 seconds total)