Starting phenix.real_space_refine on Sat Jun 7 11:38:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qfw_13950/06_2025/7qfw_13950.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qfw_13950/06_2025/7qfw_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_13950/06_2025/7qfw_13950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qfw_13950/06_2025/7qfw_13950.map" model { file = "/net/cci-nas-00/data/ceres_data/7qfw_13950/06_2025/7qfw_13950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qfw_13950/06_2025/7qfw_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-5710/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: 5.79, per 1000 atoms: 0.66 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: 2.10 Conformation dependent library (CDL) restraints added in 915.6 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: 3.02 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: 3.48 Time building geometry restraints manager: 2.52 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: 1.370 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.680 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.400 ------------------------------------------------------------------------------- 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= 0.287 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 Details of bonding type rmsd hydrogen bonds : bond 0.12665 ( 481) hydrogen bonds : angle 6.10970 ( 1368) covalent geometry : bond 0.00614 ( 9046) covalent geometry : angle 0.98408 (12494) *********************** 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 : 0.847 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: 0.2569 time to fit residues: 65.5448 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 : 0.819 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.164362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.141575 restraints weight = 12557.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.145264 restraints weight = 6749.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.147794 restraints weight = 4217.299| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 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= 0.159 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 Details of bonding type rmsd hydrogen bonds : bond 0.04992 ( 481) hydrogen bonds : angle 4.32365 ( 1368) covalent geometry : bond 0.00349 ( 9046) covalent geometry : angle 0.62827 (12494) *********************** 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 : 0.872 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7650 (mttm) cc_final: 0.7372 (mmtp) REVERT: A 13 ILE cc_start: 0.8056 (mm) cc_final: 0.7673 (mt) REVERT: A 19 GLU cc_start: 0.7083 (tt0) cc_final: 0.6842 (tt0) REVERT: A 31 HIS cc_start: 0.6931 (OUTLIER) cc_final: 0.6706 (m-70) REVERT: A 39 LYS cc_start: 0.7834 (tptt) cc_final: 0.7466 (tptt) REVERT: A 72 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7425 (tm-30) REVERT: A 107 GLU cc_start: 0.7962 (mp0) cc_final: 0.7711 (mm-30) REVERT: A 227 MET cc_start: 0.7339 (ttm) cc_final: 0.7128 (ttm) REVERT: A 333 LEU cc_start: 0.8102 (mt) cc_final: 0.7757 (tp) REVERT: A 421 ILE cc_start: 0.6544 (mt) cc_final: 0.6343 (mm) REVERT: A 692 LYS cc_start: 0.7829 (mmmt) cc_final: 0.7539 (mmmt) REVERT: A 695 LYS cc_start: 0.7006 (mttt) cc_final: 0.6765 (mttp) REVERT: A 753 VAL cc_start: 0.8004 (p) cc_final: 0.7688 (t) REVERT: A 767 ARG cc_start: 0.7663 (mtm-85) cc_final: 0.7444 (mtm-85) REVERT: A 841 GLN cc_start: 0.7567 (mt0) cc_final: 0.7311 (tt0) REVERT: A 895 LYS cc_start: 0.7536 (tttt) cc_final: 0.7274 (ttpt) REVERT: B 391 MET cc_start: 0.6388 (OUTLIER) cc_final: 0.5953 (mmt) REVERT: B 492 ASN cc_start: 0.8091 (t0) cc_final: 0.7635 (m-40) outliers start: 13 outliers final: 5 residues processed: 189 average time/residue: 0.2497 time to fit residues: 62.0852 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 : 0.810 ------------------------------------------------------------------------------- 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 59 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 0.0770 chunk 78 optimal weight: 0.7980 chunk 44 optimal weight: 0.0970 chunk 34 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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 391 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.165034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.142019 restraints weight = 12769.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.145754 restraints weight = 6869.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.148367 restraints weight = 4292.975| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.2113 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= 0.147 Angle : 0.613 7.067 12494 Z= 0.342 Chirality : 0.039 0.192 1438 Planarity : 0.005 0.054 1373 Dihedral : 24.463 139.442 1749 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.27 % Allowed : 15.87 % 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: -1.71 (0.26), residues: 905 helix: -0.40 (0.20), residues: 628 sheet: None (None), residues: 0 loop : -2.70 (0.30), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 780 HIS 0.011 0.001 HIS A 31 PHE 0.023 0.001 PHE A 808 TYR 0.013 0.001 TYR A 657 ARG 0.009 0.001 ARG A 581 Details of bonding type rmsd hydrogen bonds : bond 0.04675 ( 481) hydrogen bonds : angle 4.04134 ( 1368) covalent geometry : bond 0.00323 ( 9046) covalent geometry : angle 0.61287 (12494) *********************** 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 184 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7724 (mttm) cc_final: 0.7519 (mmtp) REVERT: A 13 ILE cc_start: 0.8058 (mm) cc_final: 0.7706 (mt) REVERT: A 19 GLU cc_start: 0.7059 (tt0) cc_final: 0.6829 (tt0) REVERT: A 39 LYS cc_start: 0.7783 (tptt) cc_final: 0.7487 (tptt) REVERT: A 291 VAL cc_start: 0.7460 (m) cc_final: 0.7054 (p) REVERT: A 333 LEU cc_start: 0.8055 (mt) cc_final: 0.7741 (tt) REVERT: A 384 GLU cc_start: 0.6721 (tm-30) cc_final: 0.6216 (tm-30) REVERT: A 641 MET cc_start: 0.7150 (tpt) cc_final: 0.6801 (tpt) REVERT: A 692 LYS cc_start: 0.7895 (mmmt) cc_final: 0.7597 (mmmt) REVERT: A 808 PHE cc_start: 0.7947 (t80) cc_final: 0.7595 (t80) REVERT: A 841 GLN cc_start: 0.7555 (mt0) cc_final: 0.7316 (tt0) REVERT: A 852 ILE cc_start: 0.7956 (mm) cc_final: 0.7745 (mm) REVERT: B 391 MET cc_start: 0.6296 (mmt) cc_final: 0.5966 (mmt) REVERT: B 408 TRP cc_start: 0.5527 (p-90) cc_final: 0.4469 (p-90) REVERT: B 492 ASN cc_start: 0.7992 (t0) cc_final: 0.7621 (m-40) outliers start: 19 outliers final: 10 residues processed: 175 average time/residue: 0.2343 time to fit residues: 54.8460 Evaluate side-chains 166 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 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 485 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.162739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.138793 restraints weight = 12659.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.142600 restraints weight = 6902.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.145078 restraints weight = 4345.036| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.2346 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= 0.182 Angle : 0.632 6.899 12494 Z= 0.351 Chirality : 0.041 0.184 1438 Planarity : 0.005 0.066 1373 Dihedral : 24.398 142.690 1749 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.74 % Allowed : 17.30 % Favored : 79.95 % 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: -1.50 (0.26), residues: 905 helix: -0.26 (0.20), residues: 633 sheet: None (None), residues: 0 loop : -2.62 (0.31), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 408 HIS 0.004 0.001 HIS A 121 PHE 0.013 0.002 PHE A 808 TYR 0.016 0.001 TYR A 657 ARG 0.011 0.001 ARG A 581 Details of bonding type rmsd hydrogen bonds : bond 0.04868 ( 481) hydrogen bonds : angle 4.04627 ( 1368) covalent geometry : bond 0.00412 ( 9046) covalent geometry : angle 0.63236 (12494) *********************** 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 184 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7582 (mttm) cc_final: 0.7198 (mttm) REVERT: A 13 ILE cc_start: 0.8097 (mm) cc_final: 0.7728 (mt) REVERT: A 19 GLU cc_start: 0.7078 (tt0) cc_final: 0.6841 (tt0) REVERT: A 39 LYS cc_start: 0.7858 (tptt) cc_final: 0.7640 (tptt) REVERT: A 72 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7109 (tm-30) REVERT: A 333 LEU cc_start: 0.8098 (mt) cc_final: 0.7713 (tp) REVERT: A 353 ASP cc_start: 0.6704 (t0) cc_final: 0.6484 (t0) REVERT: A 384 GLU cc_start: 0.7000 (tm-30) cc_final: 0.6601 (tm-30) REVERT: A 399 ARG cc_start: 0.6843 (tpt90) cc_final: 0.6364 (tpt90) REVERT: A 431 ARG cc_start: 0.5281 (mtp180) cc_final: 0.4592 (mtp180) REVERT: A 443 MET cc_start: 0.7858 (tpp) cc_final: 0.7446 (tpt) REVERT: A 689 ILE cc_start: 0.7756 (mt) cc_final: 0.7527 (mt) REVERT: A 692 LYS cc_start: 0.7924 (mmmt) cc_final: 0.7656 (mmmt) REVERT: A 841 GLN cc_start: 0.7620 (mt0) cc_final: 0.7411 (tt0) REVERT: A 852 ILE cc_start: 0.8106 (mm) cc_final: 0.7874 (mm) REVERT: B 391 MET cc_start: 0.6219 (OUTLIER) cc_final: 0.5926 (mmt) REVERT: B 492 ASN cc_start: 0.8108 (t0) cc_final: 0.7760 (m-40) outliers start: 23 outliers final: 12 residues processed: 174 average time/residue: 0.2522 time to fit residues: 59.1684 Evaluate side-chains 171 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 588 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 61 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.164647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.141876 restraints weight = 12705.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.145556 restraints weight = 6847.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.148081 restraints weight = 4277.283| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9046 Z= 0.159 Angle : 0.613 7.643 12494 Z= 0.339 Chirality : 0.040 0.186 1438 Planarity : 0.004 0.050 1373 Dihedral : 24.248 144.483 1749 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.74 % Allowed : 17.78 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.27), residues: 905 helix: -0.03 (0.21), residues: 633 sheet: None (None), residues: 0 loop : -2.60 (0.31), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 780 HIS 0.017 0.001 HIS A 391 PHE 0.022 0.001 PHE A 808 TYR 0.013 0.001 TYR A 657 ARG 0.010 0.001 ARG A 910 Details of bonding type rmsd hydrogen bonds : bond 0.04646 ( 481) hydrogen bonds : angle 3.95698 ( 1368) covalent geometry : bond 0.00360 ( 9046) covalent geometry : angle 0.61304 (12494) *********************** 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: 23 poor density : 164 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8064 (mm) cc_final: 0.7712 (mt) REVERT: A 19 GLU cc_start: 0.7006 (tt0) cc_final: 0.6804 (tt0) REVERT: A 72 GLU cc_start: 0.7713 (tm-30) cc_final: 0.6618 (tm-30) REVERT: A 288 GLU cc_start: 0.6480 (tm-30) cc_final: 0.6108 (tt0) REVERT: A 333 LEU cc_start: 0.8020 (mt) cc_final: 0.7706 (tp) REVERT: A 384 GLU cc_start: 0.6993 (tm-30) cc_final: 0.6731 (tm-30) REVERT: A 431 ARG cc_start: 0.5177 (mtp180) cc_final: 0.4524 (mtp180) REVERT: A 443 MET cc_start: 0.7809 (tpp) cc_final: 0.7354 (tpt) REVERT: A 493 ASP cc_start: 0.6610 (t0) cc_final: 0.6398 (t0) REVERT: A 584 TYR cc_start: 0.6953 (m-80) cc_final: 0.6667 (m-80) REVERT: A 641 MET cc_start: 0.6889 (tpt) cc_final: 0.6603 (tpt) REVERT: A 692 LYS cc_start: 0.7937 (mmmt) cc_final: 0.7670 (mmmt) REVERT: A 841 GLN cc_start: 0.7606 (mt0) cc_final: 0.7390 (tt0) REVERT: A 852 ILE cc_start: 0.8042 (mm) cc_final: 0.7744 (mm) REVERT: A 869 LEU cc_start: 0.7454 (mt) cc_final: 0.7148 (mt) REVERT: B 391 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.5979 (mmt) REVERT: B 492 ASN cc_start: 0.7981 (t0) cc_final: 0.7606 (m-40) outliers start: 23 outliers final: 18 residues processed: 173 average time/residue: 0.2418 time to fit residues: 55.6577 Evaluate side-chains 177 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 133 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 588 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 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 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 50 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.161374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.137582 restraints weight = 12512.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.141297 restraints weight = 6887.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.143814 restraints weight = 4389.422| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9046 Z= 0.229 Angle : 0.667 8.380 12494 Z= 0.368 Chirality : 0.043 0.163 1438 Planarity : 0.005 0.052 1373 Dihedral : 24.330 146.780 1749 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.51 % Allowed : 20.05 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.26), residues: 905 helix: -0.24 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.68 (0.30), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 809 HIS 0.005 0.001 HIS A 391 PHE 0.016 0.002 PHE A 808 TYR 0.016 0.002 TYR A 657 ARG 0.010 0.001 ARG A 910 Details of bonding type rmsd hydrogen bonds : bond 0.05213 ( 481) hydrogen bonds : angle 4.18151 ( 1368) covalent geometry : bond 0.00521 ( 9046) covalent geometry : angle 0.66739 (12494) *********************** 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 189 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7585 (mttm) cc_final: 0.7251 (mttm) REVERT: A 13 ILE cc_start: 0.8102 (mm) cc_final: 0.7751 (mt) REVERT: A 19 GLU cc_start: 0.7094 (tt0) cc_final: 0.6858 (tt0) REVERT: A 72 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7381 (tm-30) REVERT: A 146 ASP cc_start: 0.5863 (t0) cc_final: 0.5523 (t0) REVERT: A 333 LEU cc_start: 0.8108 (mt) cc_final: 0.7894 (tp) REVERT: A 399 ARG cc_start: 0.6774 (tpt90) cc_final: 0.6367 (tpt90) REVERT: A 431 ARG cc_start: 0.5144 (mtp180) cc_final: 0.4371 (mtp180) REVERT: A 443 MET cc_start: 0.7811 (tpp) cc_final: 0.7392 (tpt) REVERT: A 493 ASP cc_start: 0.6716 (t0) cc_final: 0.6500 (t0) REVERT: A 584 TYR cc_start: 0.7027 (m-80) cc_final: 0.6718 (m-80) REVERT: A 692 LYS cc_start: 0.7941 (mmmt) cc_final: 0.7674 (mmmt) REVERT: A 852 ILE cc_start: 0.8059 (mm) cc_final: 0.7814 (mm) REVERT: A 869 LEU cc_start: 0.7534 (mt) cc_final: 0.7274 (mt) REVERT: B 391 MET cc_start: 0.6172 (OUTLIER) cc_final: 0.5939 (mmt) REVERT: B 492 ASN cc_start: 0.8175 (t0) cc_final: 0.7707 (m-40) outliers start: 21 outliers final: 15 residues processed: 179 average time/residue: 0.2354 time to fit residues: 56.2940 Evaluate side-chains 174 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 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 787 VAL Chi-restraints excluded: chain A residue 791 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 462 ASP Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 16 optimal weight: 0.0870 chunk 52 optimal weight: 0.3980 chunk 66 optimal weight: 0.5980 chunk 79 optimal weight: 0.0570 chunk 29 optimal weight: 0.5980 chunk 19 optimal weight: 0.0470 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 overall best weight: 0.2374 ------------------------------------------------------------------------------- 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 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 = 0.4160 r_free = 0.4160 target = 0.166559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.143337 restraints weight = 12618.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.146967 restraints weight = 6963.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.149460 restraints weight = 4432.057| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.2957 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= 0.135 Angle : 0.612 8.993 12494 Z= 0.336 Chirality : 0.039 0.150 1438 Planarity : 0.004 0.048 1373 Dihedral : 24.085 145.254 1749 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.74 % Allowed : 21.12 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.91 (0.27), residues: 905 helix: 0.22 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -2.48 (0.31), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 780 HIS 0.006 0.001 HIS A 121 PHE 0.028 0.001 PHE A 118 TYR 0.013 0.001 TYR A 657 ARG 0.011 0.000 ARG A 910 Details of bonding type rmsd hydrogen bonds : bond 0.04379 ( 481) hydrogen bonds : angle 3.86651 ( 1368) covalent geometry : bond 0.00303 ( 9046) covalent geometry : angle 0.61196 (12494) *********************** 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 187 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8124 (mm) cc_final: 0.7764 (mt) REVERT: A 19 GLU cc_start: 0.6971 (tt0) cc_final: 0.6742 (tt0) REVERT: A 185 PHE cc_start: 0.7007 (m-80) cc_final: 0.6594 (m-10) REVERT: A 252 ARG cc_start: 0.7049 (mtm110) cc_final: 0.6717 (mtm180) REVERT: A 265 ARG cc_start: 0.8277 (mtp-110) cc_final: 0.7979 (ttm110) REVERT: A 333 LEU cc_start: 0.7907 (mt) cc_final: 0.7644 (tt) REVERT: A 431 ARG cc_start: 0.5000 (mtp180) cc_final: 0.4358 (mtp180) REVERT: A 443 MET cc_start: 0.7753 (tpp) cc_final: 0.7389 (tpt) REVERT: A 493 ASP cc_start: 0.6533 (t0) cc_final: 0.6320 (t0) REVERT: A 692 LYS cc_start: 0.7949 (mmmt) cc_final: 0.7689 (mmmt) REVERT: A 852 ILE cc_start: 0.7878 (mm) cc_final: 0.7670 (mm) REVERT: A 875 TYR cc_start: 0.7347 (m-80) cc_final: 0.7143 (m-80) REVERT: B 391 MET cc_start: 0.6133 (mmt) cc_final: 0.5897 (mmt) REVERT: B 492 ASN cc_start: 0.7791 (t0) cc_final: 0.7432 (m-40) outliers start: 23 outliers final: 14 residues processed: 175 average time/residue: 0.2451 time to fit residues: 56.4580 Evaluate side-chains 173 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 291 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ILE 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 816 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 485 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 86 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 32 optimal weight: 0.1980 chunk 70 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 ** 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 = 0.4143 r_free = 0.4143 target = 0.164852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.141138 restraints weight = 12728.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.144801 restraints weight = 7075.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.147292 restraints weight = 4534.265| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.3094 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= 0.152 Angle : 0.633 8.680 12494 Z= 0.344 Chirality : 0.040 0.194 1438 Planarity : 0.004 0.050 1373 Dihedral : 24.044 142.740 1749 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.03 % Allowed : 23.15 % 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: -0.88 (0.27), residues: 905 helix: 0.26 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -2.55 (0.31), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 351 HIS 0.015 0.001 HIS A 391 PHE 0.022 0.001 PHE A 118 TYR 0.015 0.001 TYR A 657 ARG 0.012 0.001 ARG A 910 Details of bonding type rmsd hydrogen bonds : bond 0.04416 ( 481) hydrogen bonds : angle 3.86290 ( 1368) covalent geometry : bond 0.00348 ( 9046) covalent geometry : angle 0.63344 (12494) *********************** 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 174 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7559 (mttm) cc_final: 0.7271 (mttm) REVERT: A 13 ILE cc_start: 0.8100 (mm) cc_final: 0.7758 (mt) REVERT: A 19 GLU cc_start: 0.6984 (tt0) cc_final: 0.6776 (tt0) REVERT: A 185 PHE cc_start: 0.6923 (m-80) cc_final: 0.6615 (m-10) REVERT: A 252 ARG cc_start: 0.7223 (mtm110) cc_final: 0.6943 (mtm180) REVERT: A 333 LEU cc_start: 0.7912 (mt) cc_final: 0.7652 (tt) REVERT: A 443 MET cc_start: 0.7746 (tpp) cc_final: 0.7373 (tpt) REVERT: A 493 ASP cc_start: 0.6551 (t0) cc_final: 0.6314 (t0) REVERT: A 692 LYS cc_start: 0.7937 (mmmt) cc_final: 0.7693 (mmmt) REVERT: A 852 ILE cc_start: 0.7938 (mm) cc_final: 0.7711 (mm) REVERT: B 391 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.5930 (mmt) outliers start: 17 outliers final: 13 residues processed: 164 average time/residue: 0.2465 time to fit residues: 53.6055 Evaluate side-chains 167 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE 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 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 391 MET 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 43 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 61 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.0670 chunk 68 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 overall best weight: 0.4118 ------------------------------------------------------------------------------- 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 ** 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 = 0.4155 r_free = 0.4155 target = 0.166029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.142579 restraints weight = 12734.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.146192 restraints weight = 7095.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.148766 restraints weight = 4553.379| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.3271 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= 0.145 Angle : 0.632 9.862 12494 Z= 0.341 Chirality : 0.040 0.315 1438 Planarity : 0.004 0.054 1373 Dihedral : 23.957 137.295 1749 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.79 % Allowed : 23.51 % Favored : 74.70 % 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: -0.79 (0.27), residues: 905 helix: 0.33 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -2.56 (0.31), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 780 HIS 0.006 0.001 HIS A 121 PHE 0.020 0.001 PHE A 118 TYR 0.014 0.001 TYR A 657 ARG 0.012 0.001 ARG A 910 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 481) hydrogen bonds : angle 3.82859 ( 1368) covalent geometry : bond 0.00330 ( 9046) covalent geometry : angle 0.63245 (12494) *********************** 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 174 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8096 (mm) cc_final: 0.7753 (mt) REVERT: A 185 PHE cc_start: 0.6861 (m-80) cc_final: 0.6570 (m-10) REVERT: A 265 ARG cc_start: 0.8288 (mtp-110) cc_final: 0.7968 (ttm110) REVERT: A 333 LEU cc_start: 0.7872 (mt) cc_final: 0.7625 (tt) REVERT: A 431 ARG cc_start: 0.5007 (mtp180) cc_final: 0.4255 (mtp180) REVERT: A 443 MET cc_start: 0.7749 (tpp) cc_final: 0.7375 (tpt) REVERT: A 493 ASP cc_start: 0.6520 (t0) cc_final: 0.6299 (t0) REVERT: A 692 LYS cc_start: 0.7923 (mmmt) cc_final: 0.7699 (mmmt) REVERT: A 852 ILE cc_start: 0.7932 (mm) cc_final: 0.7708 (mm) REVERT: A 869 LEU cc_start: 0.7494 (mm) cc_final: 0.6987 (mt) REVERT: B 391 MET cc_start: 0.6176 (OUTLIER) cc_final: 0.5961 (mmt) outliers start: 15 outliers final: 13 residues processed: 167 average time/residue: 0.2515 time to fit residues: 55.3828 Evaluate side-chains 169 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 471 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 660 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 888 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 391 MET 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 92 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 18 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 A 745 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.164641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.141001 restraints weight = 12582.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.144667 restraints weight = 6987.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.147236 restraints weight = 4463.084| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.3302 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= 0.163 Angle : 0.658 10.607 12494 Z= 0.355 Chirality : 0.042 0.355 1438 Planarity : 0.005 0.055 1373 Dihedral : 23.960 136.547 1749 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.79 % Allowed : 24.11 % Favored : 74.11 % 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: -0.87 (0.27), residues: 905 helix: 0.29 (0.21), residues: 637 sheet: None (None), residues: 0 loop : -2.66 (0.30), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 351 HIS 0.006 0.001 HIS A 121 PHE 0.019 0.001 PHE A 118 TYR 0.016 0.001 TYR A 657 ARG 0.013 0.001 ARG A 910 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 481) hydrogen bonds : angle 3.89959 ( 1368) covalent geometry : bond 0.00375 ( 9046) covalent geometry : angle 0.65835 (12494) ********************** 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 171 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7539 (mttm) cc_final: 0.7271 (mttm) REVERT: A 13 ILE cc_start: 0.8092 (mm) cc_final: 0.7740 (mt) REVERT: A 185 PHE cc_start: 0.6849 (m-80) cc_final: 0.6543 (m-10) REVERT: A 333 LEU cc_start: 0.7986 (mt) cc_final: 0.7651 (tp) REVERT: A 431 ARG cc_start: 0.4904 (mtp180) cc_final: 0.4165 (mtp180) REVERT: A 443 MET cc_start: 0.7740 (tpp) cc_final: 0.7355 (tpt) REVERT: A 493 ASP cc_start: 0.6545 (t0) cc_final: 0.6330 (t0) REVERT: A 692 LYS cc_start: 0.7944 (mmmt) cc_final: 0.7718 (mmmt) REVERT: A 852 ILE cc_start: 0.7950 (mm) cc_final: 0.7682 (mm) REVERT: A 869 LEU cc_start: 0.7462 (mm) cc_final: 0.6984 (mt) REVERT: B 391 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5908 (mmt) REVERT: B 408 TRP cc_start: 0.5299 (p-90) cc_final: 0.4947 (p-90) outliers start: 15 outliers final: 14 residues processed: 162 average time/residue: 0.2433 time to fit residues: 52.1000 Evaluate side-chains 170 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 340 ILE 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 660 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 888 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 391 MET 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 59 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 53 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.166129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.142513 restraints weight = 12433.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.146153 restraints weight = 6875.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.148636 restraints weight = 4380.262| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9046 Z= 0.159 Angle : 0.655 10.313 12494 Z= 0.352 Chirality : 0.041 0.347 1438 Planarity : 0.004 0.056 1373 Dihedral : 23.957 134.304 1749 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.67 % Allowed : 24.11 % Favored : 74.22 % 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: -0.86 (0.27), residues: 905 helix: 0.30 (0.21), residues: 637 sheet: None (None), residues: 0 loop : -2.63 (0.30), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 351 HIS 0.006 0.001 HIS A 121 PHE 0.018 0.001 PHE A 118 TYR 0.015 0.001 TYR A 657 ARG 0.013 0.001 ARG A 910 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 481) hydrogen bonds : angle 3.88452 ( 1368) covalent geometry : bond 0.00365 ( 9046) covalent geometry : angle 0.65517 (12494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3032.75 seconds wall clock time: 53 minutes 38.53 seconds (3218.53 seconds total)