Starting phenix.real_space_refine on Sun Aug 4 06:47:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hud_35035/08_2024/8hud_35035_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hud_35035/08_2024/8hud_35035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hud_35035/08_2024/8hud_35035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hud_35035/08_2024/8hud_35035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hud_35035/08_2024/8hud_35035_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hud_35035/08_2024/8hud_35035_neut.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1238 atoms to isotropic. 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 106 5.49 5 S 26 5.16 5 C 5114 2.51 5 N 1515 2.21 5 O 1909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 44": "NH1" <-> "NH2" Residue "A GLU 439": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8670 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 6406 Classifications: {'peptide': 767} Link IDs: {'PTRANS': 14, 'TRANS': 752} Chain breaks: 6 Chain: "B" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1526 Classifications: {'RNA': 72} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 33, 'rna3p_pyr': 34} Link IDs: {'rna2p': 5, 'rna3p': 66} Chain: "C" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 574 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "D" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 164 Classifications: {'DNA': 8} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 7} Time building chain proxies: 6.18, per 1000 atoms: 0.71 Number of scatterers: 8670 At special positions: 0 Unit cell: (82, 105.78, 134.48, 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 26 16.00 P 106 15.00 O 1909 8.00 N 1515 7.00 C 5114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 816 " - pdb=" SG CYS A 976 " distance=2.08 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1462 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 7 sheets defined 46.5% alpha, 10.3% beta 40 base pairs and 65 stacking pairs defined. Time for finding SS restraints: 3.42 Creating SS restraints... Processing helix chain 'A' and resid 38 through 71 Processing helix chain 'A' and resid 82 through 93 removed outlier: 3.928A pdb=" N THR A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 108 Processing helix chain 'A' and resid 127 through 140 removed outlier: 3.500A pdb=" N LYS A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 178 through 196 Processing helix chain 'A' and resid 201 through 213 Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.606A pdb=" N LYS A 253 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 286 removed outlier: 3.748A pdb=" N GLN A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 308 Processing helix chain 'A' and resid 312 through 322 Processing helix chain 'A' and resid 345 through 358 removed outlier: 4.281A pdb=" N THR A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 379 Processing helix chain 'A' and resid 381 through 392 Processing helix chain 'A' and resid 397 through 411 Processing helix chain 'A' and resid 412 through 415 Processing helix chain 'A' and resid 422 through 436 Proline residue: A 431 - end of helix Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 454 through 460 Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 476 through 495 Processing helix chain 'A' and resid 685 through 700 Processing helix chain 'A' and resid 845 through 858 Processing helix chain 'A' and resid 871 through 884 removed outlier: 4.037A pdb=" N ARG A 875 " --> pdb=" O PRO A 871 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP A 876 " --> pdb=" O LYS A 872 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N MET A 877 " --> pdb=" O THR A 873 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 878 " --> pdb=" O TYR A 874 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A 883 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A 884 " --> pdb=" O ILE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 931 through 935 removed outlier: 3.735A pdb=" N GLY A 935 " --> pdb=" O HIS A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 995 Processing helix chain 'A' and resid 1007 through 1011 Processing helix chain 'A' and resid 1027 through 1031 removed outlier: 3.651A pdb=" N GLU A1031 " --> pdb=" O LYS A1028 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 267 through 268 removed outlier: 3.543A pdb=" N ALA A 267 " --> pdb=" O HIS A 419 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 291 through 292 removed outlier: 3.517A pdb=" N LYS A 287 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 329 " --> pdb=" O LYS A 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 333 removed outlier: 4.376A pdb=" N ARG A 332 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 916 through 923 removed outlier: 6.575A pdb=" N LYS A 837 " --> pdb=" O SER A 921 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN A 923 " --> pdb=" O ILE A 835 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE A 835 " --> pdb=" O GLN A 923 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY A 827 " --> pdb=" O ILE A 838 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 945 " --> pdb=" O ILE A 928 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 964 through 970 removed outlier: 3.948A pdb=" N TYR A 957 " --> pdb=" O THR A1013 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR A1013 " --> pdb=" O TYR A 957 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 964 through 970 Processing sheet with id=AA7, first strand: chain 'A' and resid 1074 through 1075 removed outlier: 3.804A pdb=" N ILE A1074 " --> pdb=" O ILE A1048 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A1048 " --> pdb=" O ILE A1074 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A1039 " --> pdb=" O GLU A1049 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LYS A1051 " --> pdb=" O PHE A1037 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE A1037 " --> pdb=" O LYS A1051 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A1083 " --> pdb=" O GLN A1025 " (cutoff:3.500A) 267 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 65 stacking parallelities Total time for adding SS restraints: 3.50 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2247 1.34 - 1.46: 2793 1.46 - 1.59: 3756 1.59 - 1.71: 211 1.71 - 1.84: 41 Bond restraints: 9048 Sorted by residual: bond pdb=" O3' DG C 10 " pdb=" P DC C 11 " ideal model delta sigma weight residual 1.607 1.672 -0.065 1.50e-02 4.44e+03 1.86e+01 bond pdb=" O3' DG D 6 " pdb=" P DC D 7 " ideal model delta sigma weight residual 1.607 1.660 -0.053 1.50e-02 4.44e+03 1.25e+01 bond pdb=" CA ARG A1071 " pdb=" C ARG A1071 " ideal model delta sigma weight residual 1.524 1.482 0.042 1.31e-02 5.83e+03 1.05e+01 bond pdb=" O3' U B 32 " pdb=" P G B 33 " ideal model delta sigma weight residual 1.607 1.652 -0.045 1.50e-02 4.44e+03 9.13e+00 bond pdb=" N ILE A1053 " pdb=" CA ILE A1053 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.26e+00 ... (remaining 9043 not shown) Histogram of bond angle deviations from ideal: 98.34 - 105.47: 560 105.47 - 112.60: 4715 112.60 - 119.73: 3236 119.73 - 126.86: 3843 126.86 - 134.00: 289 Bond angle restraints: 12643 Sorted by residual: angle pdb=" O3' DG C 2 " pdb=" C3' DG C 2 " pdb=" C2' DG C 2 " ideal model delta sigma weight residual 111.50 98.34 13.16 1.50e+00 4.44e-01 7.69e+01 angle pdb=" O3' DC C 1 " pdb=" C3' DC C 1 " pdb=" C2' DC C 1 " ideal model delta sigma weight residual 111.50 100.01 11.49 1.50e+00 4.44e-01 5.86e+01 angle pdb=" N ILE A 200 " pdb=" CA ILE A 200 " pdb=" C ILE A 200 " ideal model delta sigma weight residual 109.58 116.95 -7.37 1.29e+00 6.01e-01 3.26e+01 angle pdb=" O3' DG C 10 " pdb=" C3' DG C 10 " pdb=" C2' DG C 10 " ideal model delta sigma weight residual 111.50 119.89 -8.39 1.50e+00 4.44e-01 3.13e+01 angle pdb=" C SER A 839 " pdb=" CA SER A 839 " pdb=" CB SER A 839 " ideal model delta sigma weight residual 109.37 118.96 -9.59 1.91e+00 2.74e-01 2.52e+01 ... (remaining 12638 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 4362 17.77 - 35.54: 694 35.54 - 53.31: 295 53.31 - 71.08: 122 71.08 - 88.85: 25 Dihedral angle restraints: 5498 sinusoidal: 3218 harmonic: 2280 Sorted by residual: dihedral pdb=" CB CYS A 816 " pdb=" SG CYS A 816 " pdb=" SG CYS A 976 " pdb=" CB CYS A 976 " ideal model delta sinusoidal sigma weight residual -86.00 -29.71 -56.29 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CA GLY A1030 " pdb=" C GLY A1030 " pdb=" N GLU A1031 " pdb=" CA GLU A1031 " ideal model delta harmonic sigma weight residual 180.00 155.55 24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA TYR A 158 " pdb=" C TYR A 158 " pdb=" N HIS A 159 " pdb=" CA HIS A 159 " ideal model delta harmonic sigma weight residual 180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 5495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1186 0.066 - 0.132: 179 0.132 - 0.198: 55 0.198 - 0.264: 5 0.264 - 0.330: 7 Chirality restraints: 1432 Sorted by residual: chirality pdb=" C3' DG C 2 " pdb=" C4' DG C 2 " pdb=" O3' DG C 2 " pdb=" C2' DG C 2 " both_signs ideal model delta sigma weight residual False -2.66 -2.99 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA ILE A1053 " pdb=" N ILE A1053 " pdb=" C ILE A1053 " pdb=" CB ILE A1053 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C3' DC C 1 " pdb=" C4' DC C 1 " pdb=" O3' DC C 1 " pdb=" C2' DC C 1 " both_signs ideal model delta sigma weight residual False -2.66 -2.97 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 1429 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC D 7 " 0.006 2.00e-02 2.50e+03 2.05e-02 9.49e+00 pdb=" N1 DC D 7 " 0.024 2.00e-02 2.50e+03 pdb=" C2 DC D 7 " -0.028 2.00e-02 2.50e+03 pdb=" O2 DC D 7 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DC D 7 " 0.023 2.00e-02 2.50e+03 pdb=" C4 DC D 7 " -0.016 2.00e-02 2.50e+03 pdb=" N4 DC D 7 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DC D 7 " 0.023 2.00e-02 2.50e+03 pdb=" C6 DC D 7 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 32 " -0.019 2.00e-02 2.50e+03 1.83e-02 7.56e+00 pdb=" N1 U B 32 " 0.008 2.00e-02 2.50e+03 pdb=" C2 U B 32 " 0.043 2.00e-02 2.50e+03 pdb=" O2 U B 32 " -0.010 2.00e-02 2.50e+03 pdb=" N3 U B 32 " -0.017 2.00e-02 2.50e+03 pdb=" C4 U B 32 " -0.011 2.00e-02 2.50e+03 pdb=" O4 U B 32 " -0.004 2.00e-02 2.50e+03 pdb=" C5 U B 32 " 0.013 2.00e-02 2.50e+03 pdb=" C6 U B 32 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG D 8 " -0.004 2.00e-02 2.50e+03 1.58e-02 7.51e+00 pdb=" N9 DG D 8 " -0.001 2.00e-02 2.50e+03 pdb=" C8 DG D 8 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG D 8 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG D 8 " 0.031 2.00e-02 2.50e+03 pdb=" C6 DG D 8 " -0.001 2.00e-02 2.50e+03 pdb=" O6 DG D 8 " 0.000 2.00e-02 2.50e+03 pdb=" N1 DG D 8 " -0.029 2.00e-02 2.50e+03 pdb=" C2 DG D 8 " -0.015 2.00e-02 2.50e+03 pdb=" N2 DG D 8 " 0.030 2.00e-02 2.50e+03 pdb=" N3 DG D 8 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DG D 8 " -0.000 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2295 2.81 - 3.33: 7622 3.33 - 3.85: 14998 3.85 - 4.38: 17138 4.38 - 4.90: 26612 Nonbonded interactions: 68665 Sorted by model distance: nonbonded pdb=" O GLY A 131 " pdb=" OD1 ASN A 135 " model vdw 2.284 3.040 nonbonded pdb=" OD2 ASP A 954 " pdb=" OH TYR A 988 " model vdw 2.290 3.040 nonbonded pdb=" OG SER A 268 " pdb=" OD1 ASP A 374 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR A 234 " pdb=" O4 U B 64 " model vdw 2.316 3.040 nonbonded pdb=" O ASP A 360 " pdb=" OG SER A 363 " model vdw 2.337 3.040 ... (remaining 68660 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 31.240 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 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 : 0.005 0.065 9048 Z= 0.318 Angle : 0.835 13.158 12643 Z= 0.526 Chirality : 0.058 0.330 1432 Planarity : 0.004 0.046 1206 Dihedral : 20.890 88.851 4033 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 0.56 % Allowed : 23.22 % Favored : 76.22 % 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: -1.38 (0.31), residues: 753 helix: 0.44 (0.29), residues: 319 sheet: -1.73 (0.68), residues: 52 loop : -2.05 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1067 HIS 0.009 0.002 HIS A 973 PHE 0.032 0.002 PHE A 344 TYR 0.036 0.002 TYR A 272 ARG 0.005 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 90 average time/residue: 0.2354 time to fit residues: 28.7394 Evaluate side-chains 70 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9048 Z= 0.229 Angle : 0.578 5.386 12643 Z= 0.318 Chirality : 0.039 0.160 1432 Planarity : 0.004 0.041 1206 Dihedral : 20.132 78.803 2323 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 3.64 % Allowed : 23.36 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.31), residues: 753 helix: 0.96 (0.29), residues: 320 sheet: -1.77 (0.70), residues: 56 loop : -1.98 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1067 HIS 0.009 0.001 HIS A 342 PHE 0.015 0.002 PHE A 134 TYR 0.013 0.002 TYR A 208 ARG 0.004 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 76 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.6079 (m-80) cc_final: 0.5820 (m-80) REVERT: A 981 TYR cc_start: 0.5766 (OUTLIER) cc_final: 0.4325 (m-80) outliers start: 26 outliers final: 11 residues processed: 96 average time/residue: 0.1988 time to fit residues: 26.9818 Evaluate side-chains 81 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1074 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9048 Z= 0.327 Angle : 0.664 7.340 12643 Z= 0.356 Chirality : 0.043 0.223 1432 Planarity : 0.004 0.040 1206 Dihedral : 20.017 80.533 2323 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 4.76 % Allowed : 22.94 % Favored : 72.31 % 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: -1.15 (0.30), residues: 753 helix: 0.91 (0.29), residues: 319 sheet: -1.42 (0.74), residues: 44 loop : -2.24 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 68 HIS 0.011 0.002 HIS A 342 PHE 0.020 0.002 PHE A 277 TYR 0.017 0.002 TYR A 685 ARG 0.004 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 79 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 TYR cc_start: 0.6312 (OUTLIER) cc_final: 0.5621 (m-80) REVERT: A 369 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6549 (tt) REVERT: A 403 LYS cc_start: 0.7632 (mmtt) cc_final: 0.7372 (ttpt) REVERT: A 981 TYR cc_start: 0.5995 (OUTLIER) cc_final: 0.4383 (m-80) outliers start: 34 outliers final: 21 residues processed: 107 average time/residue: 0.1936 time to fit residues: 29.3371 Evaluate side-chains 95 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 71 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1089 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 40 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 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 312 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9048 Z= 0.194 Angle : 0.551 5.307 12643 Z= 0.302 Chirality : 0.039 0.178 1432 Planarity : 0.003 0.033 1206 Dihedral : 19.757 83.822 2323 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 4.34 % Allowed : 23.64 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.89 (0.30), residues: 753 helix: 1.07 (0.29), residues: 321 sheet: -1.84 (0.74), residues: 52 loop : -1.96 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1067 HIS 0.008 0.001 HIS A 342 PHE 0.012 0.001 PHE A 277 TYR 0.010 0.001 TYR A 208 ARG 0.003 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 81 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7894 (ptp90) REVERT: A 134 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.6345 (m-80) REVERT: A 328 TYR cc_start: 0.4701 (OUTLIER) cc_final: 0.2885 (t80) REVERT: A 347 TYR cc_start: 0.6230 (OUTLIER) cc_final: 0.5675 (m-80) REVERT: A 707 LYS cc_start: 0.7851 (mmtm) cc_final: 0.7491 (mmtt) REVERT: A 981 TYR cc_start: 0.5901 (OUTLIER) cc_final: 0.4384 (m-80) REVERT: A 986 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.5780 (mp0) outliers start: 31 outliers final: 15 residues processed: 104 average time/residue: 0.2178 time to fit residues: 31.3797 Evaluate side-chains 93 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1074 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 73 optimal weight: 0.0970 chunk 20 optimal weight: 0.2980 chunk 27 optimal weight: 8.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9048 Z= 0.177 Angle : 0.534 7.092 12643 Z= 0.292 Chirality : 0.038 0.171 1432 Planarity : 0.003 0.029 1206 Dihedral : 19.612 82.535 2323 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.62 % Allowed : 23.22 % Favored : 72.17 % 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: -0.72 (0.31), residues: 753 helix: 1.22 (0.29), residues: 320 sheet: -1.73 (0.75), residues: 52 loop : -1.87 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1067 HIS 0.008 0.001 HIS A 342 PHE 0.010 0.001 PHE A 277 TYR 0.011 0.001 TYR A 272 ARG 0.003 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 77 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7863 (ptp90) REVERT: A 328 TYR cc_start: 0.4769 (OUTLIER) cc_final: 0.2964 (t80) REVERT: A 347 TYR cc_start: 0.6169 (OUTLIER) cc_final: 0.5597 (m-80) REVERT: A 707 LYS cc_start: 0.7848 (mmtm) cc_final: 0.7520 (mmtt) REVERT: A 981 TYR cc_start: 0.5808 (OUTLIER) cc_final: 0.4350 (m-80) REVERT: A 986 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.5707 (mp0) outliers start: 33 outliers final: 15 residues processed: 102 average time/residue: 0.2266 time to fit residues: 31.3108 Evaluate side-chains 94 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1074 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 38 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 43 optimal weight: 0.0060 chunk 79 optimal weight: 5.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9048 Z= 0.225 Angle : 0.573 7.941 12643 Z= 0.310 Chirality : 0.040 0.190 1432 Planarity : 0.004 0.057 1206 Dihedral : 19.601 81.548 2323 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 4.34 % Allowed : 23.36 % Favored : 72.31 % 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: -0.81 (0.30), residues: 753 helix: 1.10 (0.29), residues: 320 sheet: -1.42 (0.77), residues: 47 loop : -1.93 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A1067 HIS 0.008 0.001 HIS A 342 PHE 0.014 0.002 PHE A 277 TYR 0.014 0.002 TYR A 272 ARG 0.003 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 78 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7897 (ptp90) REVERT: A 233 ILE cc_start: 0.8441 (tp) cc_final: 0.8206 (tp) REVERT: A 313 MET cc_start: 0.4566 (ptp) cc_final: 0.4279 (ppp) REVERT: A 328 TYR cc_start: 0.5092 (OUTLIER) cc_final: 0.3119 (t80) REVERT: A 453 LYS cc_start: 0.5435 (OUTLIER) cc_final: 0.4673 (mtmt) REVERT: A 981 TYR cc_start: 0.5844 (OUTLIER) cc_final: 0.4363 (m-80) REVERT: A 986 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.5865 (mp0) outliers start: 31 outliers final: 17 residues processed: 103 average time/residue: 0.2211 time to fit residues: 31.3440 Evaluate side-chains 94 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 72 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 954 ASP Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1074 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 4.9990 chunk 46 optimal weight: 0.2980 chunk 60 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 GLN A 173 GLN A 312 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9048 Z= 0.230 Angle : 0.569 6.072 12643 Z= 0.310 Chirality : 0.039 0.173 1432 Planarity : 0.003 0.052 1206 Dihedral : 19.583 81.764 2323 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 4.06 % Allowed : 23.78 % Favored : 72.17 % 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: -0.80 (0.30), residues: 753 helix: 1.10 (0.28), residues: 320 sheet: -1.39 (0.78), residues: 47 loop : -1.92 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A1067 HIS 0.008 0.001 HIS A 342 PHE 0.012 0.002 PHE A 277 TYR 0.018 0.002 TYR A 272 ARG 0.003 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 77 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7894 (ptp90) REVERT: A 233 ILE cc_start: 0.8432 (tp) cc_final: 0.8199 (tp) REVERT: A 328 TYR cc_start: 0.5263 (OUTLIER) cc_final: 0.3485 (t80) REVERT: A 453 LYS cc_start: 0.5455 (OUTLIER) cc_final: 0.4659 (mtmt) REVERT: A 707 LYS cc_start: 0.7916 (mmtm) cc_final: 0.7621 (mmtt) REVERT: A 981 TYR cc_start: 0.5883 (OUTLIER) cc_final: 0.4361 (m-80) REVERT: A 986 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.5814 (mp0) outliers start: 29 outliers final: 22 residues processed: 103 average time/residue: 0.2174 time to fit residues: 30.5881 Evaluate side-chains 97 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 70 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1089 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.5248 > 50: distance: 26 - 41: 10.002 distance: 30 - 49: 31.904 distance: 37 - 41: 7.854 distance: 41 - 42: 22.239 distance: 42 - 43: 16.146 distance: 42 - 45: 18.751 distance: 43 - 44: 24.806 distance: 43 - 49: 37.279 distance: 45 - 46: 24.949 distance: 46 - 47: 28.556 distance: 47 - 48: 20.168 distance: 49 - 50: 18.686 distance: 50 - 53: 24.056 distance: 51 - 52: 3.759 distance: 51 - 57: 46.859 distance: 53 - 54: 21.895 distance: 54 - 55: 3.799 distance: 54 - 56: 24.630 distance: 57 - 58: 25.685 distance: 58 - 59: 37.500 distance: 58 - 61: 7.357 distance: 59 - 60: 39.341 distance: 59 - 66: 24.988 distance: 61 - 62: 42.004 distance: 62 - 63: 28.652 distance: 64 - 65: 40.265 distance: 66 - 67: 39.683 distance: 67 - 68: 17.001 distance: 67 - 70: 40.466 distance: 68 - 76: 3.203 distance: 70 - 71: 26.267 distance: 71 - 72: 38.011 distance: 72 - 74: 40.440 distance: 73 - 75: 41.689 distance: 74 - 75: 32.168 distance: 76 - 77: 40.819 distance: 77 - 78: 37.089 distance: 77 - 80: 5.676 distance: 78 - 79: 55.735 distance: 78 - 87: 21.453 distance: 80 - 81: 28.182 distance: 81 - 82: 45.867 distance: 82 - 83: 17.171 distance: 83 - 84: 16.816 distance: 84 - 85: 23.183 distance: 84 - 86: 43.788 distance: 87 - 88: 22.003 distance: 88 - 89: 12.531 distance: 89 - 90: 50.564 distance: 89 - 91: 41.051 distance: 91 - 92: 36.895 distance: 92 - 93: 5.297 distance: 92 - 95: 57.006 distance: 93 - 94: 33.675 distance: 93 - 99: 36.747 distance: 95 - 96: 56.713 distance: 95 - 97: 5.855 distance: 99 - 100: 51.545 distance: 100 - 101: 23.402 distance: 100 - 103: 41.311 distance: 101 - 102: 41.373 distance: 101 - 105: 31.113 distance: 105 - 106: 27.394 distance: 106 - 109: 30.844 distance: 107 - 108: 11.284 distance: 109 - 110: 24.970 distance: 110 - 111: 17.358 distance: 110 - 112: 28.753 distance: 111 - 113: 26.369 distance: 112 - 114: 4.758 distance: 113 - 115: 8.382 distance: 114 - 115: 45.902 distance: 115 - 116: 5.893 distance: 117 - 118: 16.260 distance: 118 - 119: 3.091 distance: 118 - 121: 6.094 distance: 119 - 125: 34.437 distance: 121 - 122: 23.936 distance: 122 - 123: 23.868 distance: 122 - 124: 12.175