Starting phenix.real_space_refine on Fri Dec 27 23:06:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij5_60616/12_2024/9ij5_60616.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij5_60616/12_2024/9ij5_60616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ij5_60616/12_2024/9ij5_60616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij5_60616/12_2024/9ij5_60616.map" model { file = "/net/cci-nas-00/data/ceres_data/9ij5_60616/12_2024/9ij5_60616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij5_60616/12_2024/9ij5_60616.cif" } resolution = 2.8 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= 0.043 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: 6 Type Number sf(0) Gaussians P 51 5.49 5 Mg 1 5.21 5 S 44 5.16 5 C 4368 2.51 5 N 1236 2.21 5 O 1439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7139 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6057 Classifications: {'peptide': 755} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 717} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 550 Classifications: {'RNA': 26} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p': 1, 'rna3p_pur': 12, 'rna3p_pyr': 12} Link IDs: {'rna2p': 1, 'rna3p': 24} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 531 Classifications: {'RNA': 25} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 22} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.83, per 1000 atoms: 0.68 Number of scatterers: 7139 At special positions: 0 Unit cell: (77.52, 86.64, 106.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 51 15.00 Mg 1 11.99 O 1439 8.00 N 1236 7.00 C 4368 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: 2.02 Conformation dependent library (CDL) restraints added in 837.5 milliseconds 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 8 sheets defined 33.2% alpha, 24.9% beta 23 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 262 through 267 Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 388 through 399 Processing helix chain 'A' and resid 402 through 412 Processing helix chain 'A' and resid 450 through 456 Processing helix chain 'A' and resid 508 through 520 removed outlier: 3.666A pdb=" N MET A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 540 Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 612 through 631 removed outlier: 3.790A pdb=" N ALA A 616 " --> pdb=" O ALA A 612 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 646 through 661 removed outlier: 3.771A pdb=" N TYR A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 686 removed outlier: 3.970A pdb=" N TYR A 679 " --> pdb=" O ARG A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 723 removed outlier: 4.127A pdb=" N VAL A 711 " --> pdb=" O ARG A 707 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 723 " --> pdb=" O MET A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 801 removed outlier: 4.092A pdb=" N LEU A 788 " --> pdb=" O ASP A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 818 No H-bonds generated for 'chain 'A' and resid 816 through 818' Processing helix chain 'A' and resid 819 through 826 Processing helix chain 'A' and resid 826 through 835 Processing helix chain 'A' and resid 836 through 838 No H-bonds generated for 'chain 'A' and resid 836 through 838' Processing helix chain 'A' and resid 916 through 928 Processing helix chain 'A' and resid 939 through 955 Processing helix chain 'A' and resid 961 through 965 Processing sheet with id=AA1, first strand: chain 'A' and resid 769 through 774 removed outlier: 3.726A pdb=" N ASP A 743 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL A 739 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N MET A 845 " --> pdb=" O ASN A 909 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN A 909 " --> pdb=" O MET A 845 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A 847 " --> pdb=" O VAL A 907 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 887 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL A 885 " --> pdb=" O CYS A 906 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N SER A 223 " --> pdb=" O ALA A 861 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR A 859 " --> pdb=" O GLY A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 337 removed outlier: 3.773A pdb=" N PHE A 341 " --> pdb=" O TYR A 361 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG A 384 " --> pdb=" O MET A 498 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N MET A 498 " --> pdb=" O ARG A 384 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ASP A 386 " --> pdb=" O SER A 496 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N SER A 496 " --> pdb=" O ASP A 386 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 499 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE A 415 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 271 through 272 removed outlier: 6.321A pdb=" N HIS A 242 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LEU A 306 " --> pdb=" O HIS A 242 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR A 244 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE A 304 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N SER A 246 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE A 302 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 429 through 431 Processing sheet with id=AA6, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AA7, first strand: chain 'A' and resid 571 through 572 Processing sheet with id=AA8, first strand: chain 'A' and resid 638 through 641 removed outlier: 6.302A pdb=" N ALA A 605 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ILE A 670 " --> pdb=" O ALA A 605 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE A 607 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL A 667 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE A 697 " --> pdb=" O VAL A 667 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS A 669 " --> pdb=" O ILE A 697 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 774 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1805 1.33 - 1.46: 1901 1.46 - 1.58: 3524 1.58 - 1.70: 101 1.70 - 1.83: 69 Bond restraints: 7400 Sorted by residual: bond pdb=" C ALA A 862 " pdb=" N PRO A 863 " ideal model delta sigma weight residual 1.336 1.370 -0.034 1.08e-02 8.57e+03 1.01e+01 bond pdb=" CB PRO A 221 " pdb=" CG PRO A 221 " ideal model delta sigma weight residual 1.492 1.642 -0.150 5.00e-02 4.00e+02 9.02e+00 bond pdb=" CG GLN A 830 " pdb=" CD GLN A 830 " ideal model delta sigma weight residual 1.516 1.445 0.071 2.50e-02 1.60e+03 8.01e+00 bond pdb=" CG LEU A 372 " pdb=" CD2 LEU A 372 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.74e+00 bond pdb=" CB LYS A 290 " pdb=" CG LYS A 290 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.81e+00 ... (remaining 7395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 9935 2.91 - 5.82: 279 5.82 - 8.72: 32 8.72 - 11.63: 13 11.63 - 14.54: 4 Bond angle restraints: 10263 Sorted by residual: angle pdb=" CA PRO A 221 " pdb=" N PRO A 221 " pdb=" CD PRO A 221 " ideal model delta sigma weight residual 112.00 97.46 14.54 1.40e+00 5.10e-01 1.08e+02 angle pdb=" CA MET A 329 " pdb=" CB MET A 329 " pdb=" CG MET A 329 " ideal model delta sigma weight residual 114.10 126.01 -11.91 2.00e+00 2.50e-01 3.55e+01 angle pdb=" C ILE A 782 " pdb=" CA ILE A 782 " pdb=" CB ILE A 782 " ideal model delta sigma weight residual 111.29 120.47 -9.18 1.64e+00 3.72e-01 3.13e+01 angle pdb=" CA LYS A 290 " pdb=" CB LYS A 290 " pdb=" CG LYS A 290 " ideal model delta sigma weight residual 114.10 125.05 -10.95 2.00e+00 2.50e-01 3.00e+01 angle pdb=" CA PRO A 468 " pdb=" N PRO A 468 " pdb=" CD PRO A 468 " ideal model delta sigma weight residual 112.00 104.72 7.28 1.40e+00 5.10e-01 2.71e+01 ... (remaining 10258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 3697 17.83 - 35.66: 551 35.66 - 53.48: 169 53.48 - 71.31: 83 71.31 - 89.14: 21 Dihedral angle restraints: 4521 sinusoidal: 2311 harmonic: 2210 Sorted by residual: dihedral pdb=" CA ILE A 231 " pdb=" C ILE A 231 " pdb=" N GLN A 232 " pdb=" CA GLN A 232 " ideal model delta harmonic sigma weight residual 180.00 154.18 25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA MET A 329 " pdb=" C MET A 329 " pdb=" N LYS A 330 " pdb=" CA LYS A 330 " ideal model delta harmonic sigma weight residual 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" C ILE A 782 " pdb=" N ILE A 782 " pdb=" CA ILE A 782 " pdb=" CB ILE A 782 " ideal model delta harmonic sigma weight residual -122.00 -132.96 10.96 0 2.50e+00 1.60e-01 1.92e+01 ... (remaining 4518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1016 0.086 - 0.173: 174 0.173 - 0.259: 10 0.259 - 0.346: 2 0.346 - 0.432: 2 Chirality restraints: 1204 Sorted by residual: chirality pdb=" CB VAL A 791 " pdb=" CA VAL A 791 " pdb=" CG1 VAL A 791 " pdb=" CG2 VAL A 791 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" CB ILE A 854 " pdb=" CA ILE A 854 " pdb=" CG1 ILE A 854 " pdb=" CG2 ILE A 854 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CB ILE A 229 " pdb=" CA ILE A 229 " pdb=" CG1 ILE A 229 " pdb=" CG2 ILE A 229 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 1201 not shown) Planarity restraints: 1111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 220 " 0.116 5.00e-02 4.00e+02 1.63e-01 4.25e+01 pdb=" N PRO A 221 " -0.281 5.00e-02 4.00e+02 pdb=" CA PRO A 221 " 0.085 5.00e-02 4.00e+02 pdb=" CD PRO A 221 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 652 " -0.209 9.50e-02 1.11e+02 9.44e-02 7.16e+00 pdb=" NE ARG A 652 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 652 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG A 652 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 652 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 467 " -0.044 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO A 468 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " -0.036 5.00e-02 4.00e+02 ... (remaining 1108 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1641 2.79 - 3.32: 5991 3.32 - 3.85: 13389 3.85 - 4.37: 15385 4.37 - 4.90: 24752 Nonbonded interactions: 61158 Sorted by model distance: nonbonded pdb=" O THR A 649 " pdb=" OG1 THR A 653 " model vdw 2.267 3.040 nonbonded pdb=" O SER A 544 " pdb=" OG1 THR A 548 " model vdw 2.300 3.040 nonbonded pdb=" O PRO A 312 " pdb=" OH TYR A 321 " model vdw 2.321 3.040 nonbonded pdb=" ND2 ASN A 322 " pdb=" O3' C C 12 " model vdw 2.340 3.120 nonbonded pdb=" O GLY A 338 " pdb=" ND2 ASN A 422 " model vdw 2.350 3.120 ... (remaining 61153 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: 0.200 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 22.410 Find NCS groups from input model: 0.140 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:11.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 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 : 0.008 0.150 7400 Z= 0.498 Angle : 1.161 14.538 10263 Z= 0.607 Chirality : 0.064 0.432 1204 Planarity : 0.010 0.163 1111 Dihedral : 19.966 89.140 3091 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.02 % Allowed : 31.92 % Favored : 67.06 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.70 % 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: -2.72 (0.27), residues: 751 helix: -1.94 (0.28), residues: 215 sheet: -0.83 (0.40), residues: 167 loop : -2.16 (0.28), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP A 639 HIS 0.013 0.002 HIS A 946 PHE 0.032 0.004 PHE A 838 TYR 0.018 0.003 TYR A 361 ARG 0.023 0.001 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.695 Fit side-chains REVERT: A 769 TRP cc_start: 0.7081 (m100) cc_final: 0.6821 (m100) REVERT: A 845 MET cc_start: 0.8302 (ttt) cc_final: 0.7968 (ttt) outliers start: 7 outliers final: 3 residues processed: 105 average time/residue: 0.9461 time to fit residues: 106.4837 Evaluate side-chains 95 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 936 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS A 555 HIS ** A 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7400 Z= 0.190 Angle : 0.615 7.731 10263 Z= 0.318 Chirality : 0.043 0.183 1204 Planarity : 0.005 0.079 1111 Dihedral : 17.624 82.068 1590 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.69 % Allowed : 31.48 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.91 (0.28), residues: 751 helix: -0.55 (0.32), residues: 221 sheet: -0.90 (0.38), residues: 176 loop : -1.89 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 639 HIS 0.003 0.001 HIS A 903 PHE 0.019 0.002 PHE A 325 TYR 0.011 0.001 TYR A 241 ARG 0.009 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.803 Fit side-chains REVERT: A 327 ARG cc_start: 0.4711 (OUTLIER) cc_final: 0.4307 (mtt-85) REVERT: A 330 LYS cc_start: 0.6509 (OUTLIER) cc_final: 0.6231 (tptt) REVERT: A 348 MET cc_start: 0.7011 (OUTLIER) cc_final: 0.6737 (pmm) REVERT: A 456 LYS cc_start: 0.6601 (OUTLIER) cc_final: 0.5784 (tptt) REVERT: A 777 MET cc_start: 0.3496 (mmp) cc_final: 0.3292 (mmt) REVERT: A 845 MET cc_start: 0.8160 (ttt) cc_final: 0.7801 (ttt) outliers start: 32 outliers final: 7 residues processed: 119 average time/residue: 0.9986 time to fit residues: 127.2690 Evaluate side-chains 99 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 910 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS A 559 HIS A 746 HIS A 801 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 7400 Z= 0.379 Angle : 0.751 7.473 10263 Z= 0.385 Chirality : 0.048 0.214 1204 Planarity : 0.005 0.039 1111 Dihedral : 17.509 81.743 1580 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 6.15 % Allowed : 29.72 % Favored : 64.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.75 (0.29), residues: 751 helix: -0.19 (0.33), residues: 215 sheet: -0.98 (0.37), residues: 178 loop : -1.85 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 639 HIS 0.013 0.002 HIS A 946 PHE 0.030 0.003 PHE A 950 TYR 0.016 0.002 TYR A 361 ARG 0.006 0.001 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 97 time to evaluate : 1.621 Fit side-chains REVERT: A 230 LYS cc_start: 0.4357 (OUTLIER) cc_final: 0.3978 (ptpp) REVERT: A 327 ARG cc_start: 0.4851 (OUTLIER) cc_final: 0.4374 (mtt-85) REVERT: A 456 LYS cc_start: 0.6657 (OUTLIER) cc_final: 0.5859 (tptt) REVERT: A 503 GLU cc_start: 0.6252 (OUTLIER) cc_final: 0.5796 (pm20) REVERT: A 666 MET cc_start: 0.6379 (OUTLIER) cc_final: 0.5656 (tpp) REVERT: A 670 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6734 (mp) REVERT: A 845 MET cc_start: 0.8138 (ttt) cc_final: 0.7752 (ttt) outliers start: 42 outliers final: 22 residues processed: 128 average time/residue: 0.9445 time to fit residues: 129.8613 Evaluate side-chains 110 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 910 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.0980 chunk 7 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 0.0060 chunk 72 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 1 optimal weight: 0.0970 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS A 385 ASN A 736 GLN A 801 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7400 Z= 0.170 Angle : 0.600 8.312 10263 Z= 0.311 Chirality : 0.044 0.214 1204 Planarity : 0.004 0.037 1111 Dihedral : 17.470 84.515 1580 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.12 % Allowed : 31.04 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.29), residues: 751 helix: 0.44 (0.34), residues: 214 sheet: -0.79 (0.39), residues: 167 loop : -1.64 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 639 HIS 0.005 0.001 HIS A 353 PHE 0.018 0.002 PHE A 341 TYR 0.012 0.001 TYR A 770 ARG 0.007 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.796 Fit side-chains REVERT: A 230 LYS cc_start: 0.3229 (OUTLIER) cc_final: 0.1989 (ptpp) REVERT: A 330 LYS cc_start: 0.6288 (OUTLIER) cc_final: 0.6080 (tptt) REVERT: A 348 MET cc_start: 0.6995 (pmm) cc_final: 0.6783 (pmm) REVERT: A 486 LYS cc_start: 0.5274 (OUTLIER) cc_final: 0.4477 (ttpt) REVERT: A 670 ILE cc_start: 0.7040 (OUTLIER) cc_final: 0.6706 (mp) REVERT: A 777 MET cc_start: 0.3458 (mmp) cc_final: 0.3161 (mmt) REVERT: A 801 ASN cc_start: 0.5198 (t0) cc_final: 0.4998 (t0) REVERT: A 845 MET cc_start: 0.7991 (ttt) cc_final: 0.7696 (ttt) REVERT: A 928 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7415 (tpt) outliers start: 35 outliers final: 13 residues processed: 131 average time/residue: 0.9989 time to fit residues: 140.3736 Evaluate side-chains 111 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 928 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 38 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7400 Z= 0.332 Angle : 0.720 12.198 10263 Z= 0.367 Chirality : 0.047 0.195 1204 Planarity : 0.005 0.040 1111 Dihedral : 17.421 82.038 1580 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 6.44 % Allowed : 30.16 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.29), residues: 751 helix: 0.36 (0.34), residues: 214 sheet: -0.89 (0.37), residues: 173 loop : -1.67 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 639 HIS 0.006 0.001 HIS A 946 PHE 0.024 0.002 PHE A 950 TYR 0.012 0.002 TYR A 361 ARG 0.009 0.001 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 95 time to evaluate : 0.731 Fit side-chains REVERT: A 230 LYS cc_start: 0.4354 (OUTLIER) cc_final: 0.3985 (ptpp) REVERT: A 254 MET cc_start: 0.5506 (pmm) cc_final: 0.5155 (pmt) REVERT: A 486 LYS cc_start: 0.5320 (OUTLIER) cc_final: 0.4574 (ttpt) REVERT: A 503 GLU cc_start: 0.6157 (OUTLIER) cc_final: 0.5748 (pm20) REVERT: A 670 ILE cc_start: 0.7203 (OUTLIER) cc_final: 0.6764 (mp) outliers start: 44 outliers final: 21 residues processed: 128 average time/residue: 0.9927 time to fit residues: 135.9703 Evaluate side-chains 114 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 910 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS A 736 GLN A 801 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7400 Z= 0.218 Angle : 0.646 8.820 10263 Z= 0.329 Chirality : 0.044 0.188 1204 Planarity : 0.005 0.061 1111 Dihedral : 17.389 84.166 1580 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 6.00 % Allowed : 31.77 % Favored : 62.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.17 (0.30), residues: 751 helix: 0.63 (0.34), residues: 212 sheet: -0.82 (0.37), residues: 175 loop : -1.60 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 639 HIS 0.005 0.001 HIS A 353 PHE 0.024 0.002 PHE A 341 TYR 0.011 0.001 TYR A 770 ARG 0.009 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 99 time to evaluate : 0.615 Fit side-chains REVERT: A 486 LYS cc_start: 0.5279 (OUTLIER) cc_final: 0.4503 (ttpt) REVERT: A 670 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6751 (mp) REVERT: A 777 MET cc_start: 0.3547 (mmp) cc_final: 0.3031 (mmt) REVERT: A 801 ASN cc_start: 0.5065 (t0) cc_final: 0.4771 (t0) REVERT: A 852 LYS cc_start: 0.6663 (OUTLIER) cc_final: 0.6415 (ttmm) outliers start: 41 outliers final: 23 residues processed: 129 average time/residue: 0.8921 time to fit residues: 123.8745 Evaluate side-chains 114 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 935 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 5.9990 chunk 64 optimal weight: 0.0030 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 47 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 353 HIS ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 7400 Z= 0.199 Angle : 0.651 8.519 10263 Z= 0.331 Chirality : 0.045 0.285 1204 Planarity : 0.004 0.039 1111 Dihedral : 17.358 84.647 1580 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.83 % Allowed : 32.94 % Favored : 62.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.10 (0.30), residues: 751 helix: 0.69 (0.35), residues: 212 sheet: -0.80 (0.37), residues: 173 loop : -1.55 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 604 HIS 0.005 0.001 HIS A 353 PHE 0.015 0.002 PHE A 950 TYR 0.012 0.001 TYR A 770 ARG 0.010 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.617 Fit side-chains REVERT: A 230 LYS cc_start: 0.4013 (OUTLIER) cc_final: 0.3279 (ptpp) REVERT: A 254 MET cc_start: 0.5364 (pmm) cc_final: 0.4932 (pmt) REVERT: A 486 LYS cc_start: 0.5284 (OUTLIER) cc_final: 0.4488 (ttpt) REVERT: A 670 ILE cc_start: 0.7095 (OUTLIER) cc_final: 0.6749 (mp) REVERT: A 777 MET cc_start: 0.3737 (mmp) cc_final: 0.3385 (mmt) outliers start: 33 outliers final: 23 residues processed: 118 average time/residue: 0.9009 time to fit residues: 115.1577 Evaluate side-chains 112 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 935 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 0.0980 chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN A 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7400 Z= 0.234 Angle : 0.683 8.417 10263 Z= 0.346 Chirality : 0.045 0.265 1204 Planarity : 0.004 0.040 1111 Dihedral : 17.331 84.024 1580 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.12 % Allowed : 33.82 % Favored : 61.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.30), residues: 751 helix: 0.71 (0.35), residues: 212 sheet: -0.79 (0.37), residues: 175 loop : -1.53 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 639 HIS 0.007 0.001 HIS A 946 PHE 0.031 0.002 PHE A 950 TYR 0.010 0.001 TYR A 770 ARG 0.010 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.917 Fit side-chains REVERT: A 486 LYS cc_start: 0.5362 (OUTLIER) cc_final: 0.4536 (ttpt) REVERT: A 670 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6763 (mp) REVERT: A 777 MET cc_start: 0.3686 (mmp) cc_final: 0.3416 (mmt) outliers start: 35 outliers final: 20 residues processed: 118 average time/residue: 0.8372 time to fit residues: 107.1552 Evaluate side-chains 112 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 935 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7400 Z= 0.238 Angle : 0.687 8.924 10263 Z= 0.348 Chirality : 0.045 0.249 1204 Planarity : 0.004 0.040 1111 Dihedral : 17.318 84.043 1580 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.25 % Allowed : 34.55 % Favored : 61.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.04 (0.30), residues: 751 helix: 0.67 (0.35), residues: 213 sheet: -0.80 (0.38), residues: 175 loop : -1.45 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 639 HIS 0.010 0.001 HIS A 946 PHE 0.033 0.002 PHE A 950 TYR 0.011 0.002 TYR A 770 ARG 0.011 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.669 Fit side-chains REVERT: A 254 MET cc_start: 0.5408 (pmm) cc_final: 0.4958 (pmt) REVERT: A 486 LYS cc_start: 0.5380 (OUTLIER) cc_final: 0.4539 (ttpt) REVERT: A 503 GLU cc_start: 0.5995 (OUTLIER) cc_final: 0.5641 (pm20) REVERT: A 670 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6739 (mp) REVERT: A 777 MET cc_start: 0.3664 (mmp) cc_final: 0.3427 (mmt) outliers start: 29 outliers final: 21 residues processed: 118 average time/residue: 0.9245 time to fit residues: 117.2912 Evaluate side-chains 114 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 935 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 62 optimal weight: 0.0980 chunk 6 optimal weight: 0.0980 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7400 Z= 0.204 Angle : 0.670 9.140 10263 Z= 0.342 Chirality : 0.045 0.246 1204 Planarity : 0.005 0.047 1111 Dihedral : 17.289 86.192 1580 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.95 % Allowed : 35.14 % Favored : 60.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.02 (0.30), residues: 751 helix: 0.72 (0.35), residues: 213 sheet: -0.80 (0.37), residues: 178 loop : -1.44 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 604 HIS 0.007 0.001 HIS A 946 PHE 0.031 0.002 PHE A 950 TYR 0.012 0.001 TYR A 770 ARG 0.013 0.000 ARG A 646 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.654 Fit side-chains REVERT: A 254 MET cc_start: 0.5290 (pmm) cc_final: 0.4948 (pmt) REVERT: A 486 LYS cc_start: 0.5386 (OUTLIER) cc_final: 0.4584 (ttpt) REVERT: A 503 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.5645 (pm20) REVERT: A 670 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6727 (mp) outliers start: 27 outliers final: 21 residues processed: 108 average time/residue: 0.8872 time to fit residues: 103.5999 Evaluate side-chains 108 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 935 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN A 353 HIS ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.200581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.163740 restraints weight = 8349.353| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.16 r_work: 0.3994 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3869 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7400 Z= 0.261 Angle : 0.701 8.879 10263 Z= 0.357 Chirality : 0.046 0.233 1204 Planarity : 0.005 0.044 1111 Dihedral : 17.263 83.103 1580 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.39 % Allowed : 34.55 % Favored : 61.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.09 (0.30), residues: 751 helix: 0.71 (0.35), residues: 213 sheet: -0.85 (0.38), residues: 176 loop : -1.52 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 639 HIS 0.006 0.001 HIS A 946 PHE 0.046 0.002 PHE A 950 TYR 0.010 0.002 TYR A 770 ARG 0.012 0.001 ARG A 646 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2594.55 seconds wall clock time: 48 minutes 12.84 seconds (2892.84 seconds total)