Starting phenix.real_space_refine on Wed Sep 17 08:02:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij5_60616/09_2025/9ij5_60616.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij5_60616/09_2025/9ij5_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ij5_60616/09_2025/9ij5_60616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij5_60616/09_2025/9ij5_60616.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ij5_60616/09_2025/9ij5_60616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij5_60616/09_2025/9ij5_60616.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.80, per 1000 atoms: 0.25 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: 0.67 Conformation dependent library (CDL) restraints added in 341.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.87 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: 1.40 Time building geometry restraints manager: 0.85 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.250 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.450 ------------------------------------------------------------------------------- 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= 0.326 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.023 0.001 ARG A 652 TYR 0.018 0.003 TYR A 361 PHE 0.032 0.004 PHE A 838 TRP 0.032 0.004 TRP A 639 HIS 0.013 0.002 HIS A 946 Details of bonding type rmsd covalent geometry : bond 0.00757 ( 7400) covalent geometry : angle 1.16102 (10263) hydrogen bonds : bond 0.13882 ( 320) hydrogen bonds : angle 7.79570 ( 886) *********************** 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 : 0.236 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: 0.4451 time to fit residues: 49.9384 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 : 0.194 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.212515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.177380 restraints weight = 8516.071| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 2.16 r_work: 0.4186 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4074 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7400 Z= 0.129 Angle : 0.613 7.760 10263 Z= 0.317 Chirality : 0.043 0.184 1204 Planarity : 0.005 0.081 1111 Dihedral : 17.648 81.957 1590 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.69 % Allowed : 30.75 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.28), residues: 751 helix: -0.57 (0.32), residues: 221 sheet: -0.89 (0.38), residues: 176 loop : -1.89 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 652 TYR 0.012 0.001 TYR A 241 PHE 0.019 0.002 PHE A 325 TRP 0.014 0.001 TRP A 639 HIS 0.004 0.001 HIS A 903 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7400) covalent geometry : angle 0.61312 (10263) hydrogen bonds : bond 0.03813 ( 320) hydrogen bonds : angle 5.81184 ( 886) *********************** 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 : 0.246 Fit side-chains REVERT: A 330 LYS cc_start: 0.6328 (OUTLIER) cc_final: 0.5976 (tptt) REVERT: A 348 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6754 (pmm) REVERT: A 456 LYS cc_start: 0.6688 (OUTLIER) cc_final: 0.5273 (tptt) REVERT: A 473 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6972 (ptp90) REVERT: A 505 MET cc_start: 0.7241 (ttt) cc_final: 0.6954 (ttt) REVERT: A 736 GLN cc_start: 0.6461 (OUTLIER) cc_final: 0.6182 (mm110) REVERT: A 777 MET cc_start: 0.2903 (mmp) cc_final: 0.2595 (mmt) REVERT: A 801 ASN cc_start: 0.5409 (t0) cc_final: 0.5060 (t0) REVERT: A 845 MET cc_start: 0.8467 (ttt) cc_final: 0.8113 (ttt) outliers start: 32 outliers final: 8 residues processed: 119 average time/residue: 0.4483 time to fit residues: 56.9683 Evaluate side-chains 98 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 VAL 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 473 ARG Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 736 GLN 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 47 optimal weight: 0.0010 chunk 0 optimal weight: 30.0000 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 1 optimal weight: 0.0000 chunk 43 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.210547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.175087 restraints weight = 8316.957| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 2.12 r_work: 0.4163 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4050 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7400 Z= 0.139 Angle : 0.607 6.435 10263 Z= 0.313 Chirality : 0.044 0.168 1204 Planarity : 0.004 0.038 1111 Dihedral : 17.492 81.878 1580 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.56 % Allowed : 29.43 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.29), residues: 751 helix: 0.05 (0.33), residues: 221 sheet: -0.81 (0.39), residues: 167 loop : -1.72 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 646 TYR 0.011 0.001 TYR A 241 PHE 0.019 0.002 PHE A 325 TRP 0.011 0.001 TRP A 639 HIS 0.007 0.001 HIS A 946 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7400) covalent geometry : angle 0.60734 (10263) hydrogen bonds : bond 0.03692 ( 320) hydrogen bonds : angle 5.56735 ( 886) *********************** 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 135 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 0.238 Fit side-chains REVERT: A 230 LYS cc_start: 0.3533 (OUTLIER) cc_final: 0.2125 (ptpp) REVERT: A 327 ARG cc_start: 0.5314 (OUTLIER) cc_final: 0.4796 (mtt-85) REVERT: A 348 MET cc_start: 0.7345 (pmm) cc_final: 0.7094 (pmm) REVERT: A 456 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.5365 (tptt) REVERT: A 503 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6033 (pm20) REVERT: A 505 MET cc_start: 0.7258 (ttt) cc_final: 0.7046 (ttt) REVERT: A 646 ARG cc_start: 0.5746 (mtm110) cc_final: 0.5258 (mtm110) REVERT: A 670 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.7141 (mp) REVERT: A 682 ILE cc_start: 0.6657 (mp) cc_final: 0.6428 (mp) REVERT: A 736 GLN cc_start: 0.6674 (OUTLIER) cc_final: 0.6333 (mm110) REVERT: A 777 MET cc_start: 0.2797 (mmp) cc_final: 0.2503 (mmt) REVERT: A 801 ASN cc_start: 0.5494 (t0) cc_final: 0.4900 (t0) REVERT: A 928 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7748 (tpt) outliers start: 38 outliers final: 19 residues processed: 125 average time/residue: 0.3982 time to fit residues: 53.5051 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 : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 327 ARG 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 670 ILE Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 736 GLN 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 875 VAL 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 Chi-restraints excluded: chain A residue 928 MET Chi-restraints excluded: chain A residue 935 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 353 HIS A 746 HIS A 946 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.207920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.173678 restraints weight = 8458.192| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 1.99 r_work: 0.4211 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4102 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7400 Z= 0.195 Angle : 0.669 9.360 10263 Z= 0.342 Chirality : 0.045 0.184 1204 Planarity : 0.004 0.039 1111 Dihedral : 17.437 82.637 1580 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 6.59 % Allowed : 29.87 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.29), residues: 751 helix: 0.38 (0.34), residues: 215 sheet: -0.88 (0.38), residues: 171 loop : -1.65 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 652 TYR 0.012 0.002 TYR A 745 PHE 0.021 0.002 PHE A 341 TRP 0.011 0.002 TRP A 639 HIS 0.005 0.001 HIS A 903 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 7400) covalent geometry : angle 0.66859 (10263) hydrogen bonds : bond 0.04016 ( 320) hydrogen bonds : angle 5.59146 ( 886) *********************** 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 154 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 109 time to evaluate : 0.154 Fit side-chains REVERT: A 230 LYS cc_start: 0.4190 (OUTLIER) cc_final: 0.2673 (ptpp) REVERT: A 305 GLN cc_start: 0.7414 (tp40) cc_final: 0.6906 (tp40) REVERT: A 473 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.7036 (ptp90) REVERT: A 503 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5954 (pm20) REVERT: A 648 GLU cc_start: 0.7116 (mp0) cc_final: 0.6402 (tt0) REVERT: A 670 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7197 (mp) REVERT: A 682 ILE cc_start: 0.6996 (mp) cc_final: 0.6721 (mp) REVERT: A 777 MET cc_start: 0.3031 (mmp) cc_final: 0.2737 (mmt) REVERT: A 801 ASN cc_start: 0.5390 (t0) cc_final: 0.4789 (t0) outliers start: 45 outliers final: 18 residues processed: 141 average time/residue: 0.4724 time to fit residues: 71.0729 Evaluate side-chains 118 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 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 473 ARG 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 263 GLN A 322 ASN A 353 HIS A 946 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.203280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.168607 restraints weight = 8573.486| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 1.99 r_work: 0.4093 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3971 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 7400 Z= 0.253 Angle : 0.745 12.202 10263 Z= 0.381 Chirality : 0.048 0.217 1204 Planarity : 0.005 0.071 1111 Dihedral : 17.467 83.615 1580 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 7.17 % Allowed : 30.01 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.29), residues: 751 helix: 0.15 (0.33), residues: 218 sheet: -1.05 (0.38), residues: 175 loop : -1.70 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 646 TYR 0.014 0.002 TYR A 458 PHE 0.023 0.003 PHE A 950 TRP 0.009 0.002 TRP A 639 HIS 0.005 0.001 HIS A 865 Details of bonding type rmsd covalent geometry : bond 0.00568 ( 7400) covalent geometry : angle 0.74461 (10263) hydrogen bonds : bond 0.04487 ( 320) hydrogen bonds : angle 5.75997 ( 886) *********************** 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 153 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 104 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 254 MET cc_start: 0.6120 (pmm) cc_final: 0.5792 (pmt) REVERT: A 288 GLU cc_start: 0.6992 (mp0) cc_final: 0.6490 (tp30) REVERT: A 290 LYS cc_start: 0.8087 (mmtt) cc_final: 0.7716 (mmpt) REVERT: A 305 GLN cc_start: 0.7523 (tp40) cc_final: 0.7014 (tp40) REVERT: A 330 LYS cc_start: 0.6797 (OUTLIER) cc_final: 0.6404 (tptt) REVERT: A 486 LYS cc_start: 0.5442 (OUTLIER) cc_final: 0.4195 (ttpt) REVERT: A 503 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5951 (pm20) REVERT: A 599 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7621 (pt) REVERT: A 670 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7121 (mp) REVERT: A 801 ASN cc_start: 0.5737 (t0) cc_final: 0.5154 (t0) REVERT: A 852 LYS cc_start: 0.6799 (OUTLIER) cc_final: 0.6478 (ttmm) REVERT: A 878 THR cc_start: 0.8431 (m) cc_final: 0.8132 (m) outliers start: 49 outliers final: 23 residues processed: 140 average time/residue: 0.4430 time to fit residues: 66.2822 Evaluate side-chains 129 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 330 LYS 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 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 599 ILE Chi-restraints excluded: chain A residue 647 ILE 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 60 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 0.0870 chunk 17 optimal weight: 3.9990 chunk 48 optimal weight: 0.0980 chunk 75 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.211240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.178201 restraints weight = 8435.763| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 1.99 r_work: 0.4262 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4155 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7400 Z= 0.132 Angle : 0.626 8.132 10263 Z= 0.320 Chirality : 0.044 0.210 1204 Planarity : 0.005 0.047 1111 Dihedral : 17.403 85.471 1580 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.42 % Allowed : 32.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.30), residues: 751 helix: 0.66 (0.34), residues: 215 sheet: -0.78 (0.39), residues: 165 loop : -1.53 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 564 TYR 0.013 0.001 TYR A 770 PHE 0.022 0.002 PHE A 341 TRP 0.013 0.001 TRP A 639 HIS 0.005 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 7400) covalent geometry : angle 0.62553 (10263) hydrogen bonds : bond 0.03534 ( 320) hydrogen bonds : angle 5.45837 ( 886) *********************** 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 146 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 230 LYS cc_start: 0.4745 (OUTLIER) cc_final: 0.3992 (pttm) REVERT: A 231 ILE cc_start: 0.2193 (OUTLIER) cc_final: 0.1978 (mt) REVERT: A 288 GLU cc_start: 0.6948 (mp0) cc_final: 0.6608 (tp30) REVERT: A 305 GLN cc_start: 0.7543 (tp40) cc_final: 0.7077 (tp40) REVERT: A 330 LYS cc_start: 0.6302 (OUTLIER) cc_final: 0.6053 (tptt) REVERT: A 348 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6819 (pmm) REVERT: A 512 MET cc_start: 0.7899 (mmm) cc_final: 0.7629 (mmm) REVERT: A 599 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7232 (pt) REVERT: A 670 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7245 (mp) REVERT: A 777 MET cc_start: 0.2949 (mmp) cc_final: 0.2510 (mmt) REVERT: A 801 ASN cc_start: 0.5778 (t0) cc_final: 0.5192 (t0) REVERT: A 878 THR cc_start: 0.8247 (m) cc_final: 0.7988 (m) outliers start: 37 outliers final: 18 residues processed: 134 average time/residue: 0.4401 time to fit residues: 63.0870 Evaluate side-chains 122 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 348 MET 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 599 ILE Chi-restraints excluded: chain A residue 647 ILE 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 Chi-restraints excluded: chain A residue 917 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.211655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.177299 restraints weight = 8481.830| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 2.04 r_work: 0.4252 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4144 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7400 Z= 0.139 Angle : 0.639 8.062 10263 Z= 0.325 Chirality : 0.044 0.189 1204 Planarity : 0.004 0.045 1111 Dihedral : 17.347 83.562 1580 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.69 % Allowed : 33.97 % Favored : 61.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.30), residues: 751 helix: 0.78 (0.35), residues: 214 sheet: -0.79 (0.38), residues: 167 loop : -1.47 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 564 TYR 0.011 0.001 TYR A 770 PHE 0.013 0.002 PHE A 325 TRP 0.011 0.001 TRP A 639 HIS 0.005 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7400) covalent geometry : angle 0.63870 (10263) hydrogen bonds : bond 0.03496 ( 320) hydrogen bonds : angle 5.40003 ( 886) *********************** 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 133 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 230 LYS cc_start: 0.4462 (OUTLIER) cc_final: 0.3450 (ptpp) REVERT: A 268 ASN cc_start: 0.5872 (m-40) cc_final: 0.4804 (p0) REVERT: A 288 GLU cc_start: 0.6763 (mp0) cc_final: 0.6516 (tp30) REVERT: A 305 GLN cc_start: 0.7426 (tp40) cc_final: 0.6935 (tp40) REVERT: A 348 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.6948 (pmm) REVERT: A 599 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7183 (pt) REVERT: A 670 ILE cc_start: 0.7519 (OUTLIER) cc_final: 0.7162 (mp) REVERT: A 777 MET cc_start: 0.3115 (mmp) cc_final: 0.2739 (mmt) REVERT: A 801 ASN cc_start: 0.5772 (t0) cc_final: 0.5236 (t0) REVERT: A 878 THR cc_start: 0.8230 (m) cc_final: 0.7944 (m) outliers start: 32 outliers final: 17 residues processed: 121 average time/residue: 0.4194 time to fit residues: 54.3623 Evaluate side-chains 117 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 286 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 424 THR 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 599 ILE Chi-restraints excluded: chain A residue 647 ILE 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 353 HIS A 840 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.208255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.172813 restraints weight = 8389.553| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 2.18 r_work: 0.4164 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.4053 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7400 Z= 0.145 Angle : 0.650 8.818 10263 Z= 0.330 Chirality : 0.045 0.309 1204 Planarity : 0.005 0.050 1111 Dihedral : 17.318 84.803 1580 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.54 % Allowed : 34.85 % Favored : 60.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.30), residues: 751 helix: 0.85 (0.35), residues: 213 sheet: -0.85 (0.37), residues: 178 loop : -1.36 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 564 TYR 0.011 0.001 TYR A 770 PHE 0.020 0.002 PHE A 341 TRP 0.008 0.001 TRP A 884 HIS 0.005 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7400) covalent geometry : angle 0.65033 (10263) hydrogen bonds : bond 0.03497 ( 320) hydrogen bonds : angle 5.38215 ( 886) *********************** 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 131 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.4460 (OUTLIER) cc_final: 0.3376 (ptpp) REVERT: A 254 MET cc_start: 0.5748 (pmm) cc_final: 0.5378 (pmt) REVERT: A 288 GLU cc_start: 0.6887 (mp0) cc_final: 0.6430 (tp30) REVERT: A 290 LYS cc_start: 0.8062 (mmtt) cc_final: 0.7651 (mmpt) REVERT: A 305 GLN cc_start: 0.7306 (tp40) cc_final: 0.6725 (tp40) REVERT: A 348 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.6898 (pmm) REVERT: A 599 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7258 (pt) REVERT: A 670 ILE cc_start: 0.7489 (OUTLIER) cc_final: 0.7170 (mp) REVERT: A 682 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6546 (mp) REVERT: A 777 MET cc_start: 0.3011 (mmp) cc_final: 0.2739 (mmt) REVERT: A 801 ASN cc_start: 0.5839 (t0) cc_final: 0.5257 (t0) REVERT: A 878 THR cc_start: 0.8230 (m) cc_final: 0.7933 (m) REVERT: A 942 CYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8130 (m) outliers start: 31 outliers final: 20 residues processed: 121 average time/residue: 0.4018 time to fit residues: 52.3256 Evaluate side-chains 120 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 286 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 492 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 682 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 820 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 942 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 74 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 353 HIS A 840 ASN A 946 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.203108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.167283 restraints weight = 8379.743| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.11 r_work: 0.4097 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3987 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7400 Z= 0.214 Angle : 0.733 9.005 10263 Z= 0.371 Chirality : 0.047 0.286 1204 Planarity : 0.005 0.054 1111 Dihedral : 17.333 82.725 1580 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.98 % Allowed : 35.14 % Favored : 59.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.30), residues: 751 helix: 0.49 (0.34), residues: 214 sheet: -1.02 (0.38), residues: 180 loop : -1.45 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 564 TYR 0.011 0.002 TYR A 241 PHE 0.020 0.002 PHE A 887 TRP 0.010 0.002 TRP A 604 HIS 0.006 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 7400) covalent geometry : angle 0.73260 (10263) hydrogen bonds : bond 0.04055 ( 320) hydrogen bonds : angle 5.57932 ( 886) *********************** 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 131 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 230 LYS cc_start: 0.5085 (OUTLIER) cc_final: 0.3165 (ptpp) REVERT: A 254 MET cc_start: 0.5860 (pmm) cc_final: 0.5491 (pmt) REVERT: A 268 ASN cc_start: 0.6574 (m-40) cc_final: 0.5434 (p0) REVERT: A 288 GLU cc_start: 0.6867 (mp0) cc_final: 0.6484 (pm20) REVERT: A 290 LYS cc_start: 0.8073 (mmtt) cc_final: 0.7759 (mmpt) REVERT: A 305 GLN cc_start: 0.7335 (tp40) cc_final: 0.6781 (tp40) REVERT: A 599 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7455 (pt) REVERT: A 613 MET cc_start: 0.5414 (mmp) cc_final: 0.4907 (mpt) REVERT: A 670 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7191 (mp) REVERT: A 682 ILE cc_start: 0.6915 (OUTLIER) cc_final: 0.6516 (mp) REVERT: A 777 MET cc_start: 0.3120 (mmp) cc_final: 0.2819 (mmt) REVERT: A 801 ASN cc_start: 0.5846 (t0) cc_final: 0.5299 (t0) REVERT: A 878 THR cc_start: 0.8384 (m) cc_final: 0.8094 (m) outliers start: 34 outliers final: 22 residues processed: 122 average time/residue: 0.3730 time to fit residues: 49.0715 Evaluate side-chains 122 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 324 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 492 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 682 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 820 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 13 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 353 HIS A 840 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.205713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.170509 restraints weight = 8397.266| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 2.10 r_work: 0.4128 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.4018 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7400 Z= 0.163 Angle : 0.684 8.793 10263 Z= 0.347 Chirality : 0.046 0.287 1204 Planarity : 0.005 0.055 1111 Dihedral : 17.320 83.963 1580 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.95 % Allowed : 36.02 % Favored : 60.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.30), residues: 751 helix: 0.61 (0.34), residues: 213 sheet: -0.95 (0.38), residues: 171 loop : -1.41 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 564 TYR 0.012 0.002 TYR A 770 PHE 0.018 0.002 PHE A 887 TRP 0.011 0.002 TRP A 604 HIS 0.005 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 7400) covalent geometry : angle 0.68386 (10263) hydrogen bonds : bond 0.03644 ( 320) hydrogen bonds : angle 5.51268 ( 886) ********************** 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 125 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 ASN cc_start: 0.6415 (m-40) cc_final: 0.5299 (p0) REVERT: A 288 GLU cc_start: 0.6849 (mp0) cc_final: 0.6506 (pm20) REVERT: A 290 LYS cc_start: 0.7956 (mmtt) cc_final: 0.7716 (mmpt) REVERT: A 305 GLN cc_start: 0.7320 (tp40) cc_final: 0.6761 (tp40) REVERT: A 599 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7362 (pt) REVERT: A 613 MET cc_start: 0.5310 (mmp) cc_final: 0.4837 (mpt) REVERT: A 670 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7146 (mp) REVERT: A 682 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6535 (mp) REVERT: A 777 MET cc_start: 0.3100 (mmp) cc_final: 0.2845 (mmt) REVERT: A 801 ASN cc_start: 0.5816 (t0) cc_final: 0.5263 (t0) REVERT: A 878 THR cc_start: 0.8334 (m) cc_final: 0.8063 (m) outliers start: 27 outliers final: 20 residues processed: 117 average time/residue: 0.4459 time to fit residues: 55.9994 Evaluate side-chains 115 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 324 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 429 ASP 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 599 ILE Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 682 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 820 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 22 optimal weight: 3.9990 chunk 48 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 457 ASN A 736 GLN A 840 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.210654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.175624 restraints weight = 8319.445| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 2.19 r_work: 0.4190 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4078 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7400 Z= 0.133 Angle : 0.648 8.476 10263 Z= 0.329 Chirality : 0.045 0.278 1204 Planarity : 0.004 0.042 1111 Dihedral : 17.277 86.797 1580 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.39 % Allowed : 35.29 % Favored : 60.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.30), residues: 751 helix: 0.78 (0.35), residues: 213 sheet: -0.87 (0.38), residues: 173 loop : -1.35 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 646 TYR 0.014 0.001 TYR A 770 PHE 0.019 0.002 PHE A 341 TRP 0.009 0.001 TRP A 604 HIS 0.004 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7400) covalent geometry : angle 0.64843 (10263) hydrogen bonds : bond 0.03461 ( 320) hydrogen bonds : angle 5.37741 ( 886) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2590.65 seconds wall clock time: 45 minutes 2.65 seconds (2702.65 seconds total)