Starting phenix.real_space_refine on Tue Aug 4 21:36:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij5_60616/08_2026/9ij5_60616.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij5_60616/08_2026/9ij5_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_60616/08_2026/9ij5_60616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij5_60616/08_2026/9ij5_60616.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ij5_60616/08_2026/9ij5_60616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij5_60616/08_2026/9ij5_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: 1.33, per 1000 atoms: 0.19 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: 0.46 Conformation dependent library (CDL) restraints added in 325.5 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: 1.20 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: 1.47 Time building geometry restraints manager: 0.66 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=" C4 U C 18 " pdb=" C5 U C 18 " ideal model delta sigma weight residual 1.431 1.402 0.029 9.00e-03 1.23e+04 1.07e+01 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=" C4 C C 13 " pdb=" C5 C C 13 " ideal model delta sigma weight residual 1.425 1.404 0.021 8.00e-03 1.56e+04 6.70e+00 ... (remaining 7395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 9919 2.91 - 5.82: 295 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=" N1 C B 11 " pdb=" C6 C B 11 " pdb=" C5 C B 11 " ideal model delta sigma weight residual 121.00 125.07 -4.07 5.00e-01 4.00e+00 6.62e+01 angle pdb=" C2 C B 11 " pdb=" N1 C B 11 " pdb=" C6 C B 11 " ideal model delta sigma weight residual 120.30 117.46 2.84 4.00e-01 6.25e+00 5.03e+01 angle pdb=" C2 C C 12 " pdb=" N1 C C 12 " pdb=" C6 C C 12 " ideal model delta sigma weight residual 120.30 117.70 2.60 4.00e-01 6.25e+00 4.22e+01 angle pdb=" C2 C B 8 " pdb=" N1 C B 8 " pdb=" C6 C B 8 " ideal model delta sigma weight residual 120.30 117.76 2.54 4.00e-01 6.25e+00 4.05e+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: 966 0.086 - 0.173: 221 0.173 - 0.259: 13 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: 0.310 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.890 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:9.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 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= 0.389 Angle : 1.198 14.538 10263 Z= 0.788 Chirality : 0.069 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 are 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/Z covalent geometry : bond 0.00760 / 0.39 ( 7400) covalent geometry : angle 1.19759 / 0.79 (10263) hydrogen bonds : bond 0.13882 / 9.20 ( 320) hydrogen bonds : angle 7.79570 / 5.47 ( 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 : 0.269 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: 0.3774 time to fit residues: 42.3405 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 : 0.187 ------------------------------------------------------------------------------- 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... A 555 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.211991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.176622 restraints weight = 8500.174| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 2.15 r_work: 0.4173 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4062 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7400 Z= 0.138 Angle : 0.643 8.537 10263 Z= 0.342 Chirality : 0.044 0.188 1204 Planarity : 0.006 0.081 1111 Dihedral : 17.698 80.103 1590 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.83 % Allowed : 30.01 % Favored : 65.15 % 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 are not related in a simple way. whole: -2.07 (0.28), residues: 751 helix: -0.81 (0.31), residues: 221 sheet: -0.90 (0.38), residues: 176 loop : -1.95 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 652 TYR 0.014 0.001 TYR A 241 PHE 0.020 0.002 PHE A 950 TRP 0.017 0.001 TRP A 639 HIS 0.004 0.001 HIS A 958 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 7400) covalent geometry : angle 0.64314 / 0.34 (10263) hydrogen bonds : bond 0.04708 / 3.34 ( 320) hydrogen bonds : angle 6.07739 / 4.23 ( 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: 33 poor density : 97 time to evaluate : 0.176 Fit side-chains REVERT: A 348 MET cc_start: 0.7363 (pmm) cc_final: 0.7106 (pmm) REVERT: A 456 LYS cc_start: 0.6688 (OUTLIER) cc_final: 0.5307 (tptt) REVERT: A 513 LYS cc_start: 0.6752 (tttm) cc_final: 0.6038 (ttpm) REVERT: A 736 GLN cc_start: 0.6524 (OUTLIER) cc_final: 0.6254 (mm110) REVERT: A 773 VAL cc_start: 0.7179 (OUTLIER) cc_final: 0.6947 (p) REVERT: A 777 MET cc_start: 0.3085 (mmp) cc_final: 0.2724 (mmt) REVERT: A 801 ASN cc_start: 0.5302 (t0) cc_final: 0.4653 (t0) REVERT: A 845 MET cc_start: 0.8440 (ttt) cc_final: 0.8146 (ttt) outliers start: 33 outliers final: 10 residues processed: 119 average time/residue: 0.3712 time to fit residues: 47.3951 Evaluate side-chains 105 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 456 LYS Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 752 MET Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 935 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 47 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 38 optimal weight: 0.2980 chunk 35 optimal weight: 4.9990 chunk 1 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.210530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.175242 restraints weight = 8357.173| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.11 r_work: 0.4164 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4051 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.1318 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= 0.137 Angle : 0.615 7.999 10263 Z= 0.322 Chirality : 0.044 0.150 1204 Planarity : 0.005 0.041 1111 Dihedral : 17.507 79.364 1580 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 6.15 % Allowed : 29.14 % Favored : 64.71 % 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 are not related in a simple way. whole: -1.66 (0.29), residues: 751 helix: -0.25 (0.33), residues: 222 sheet: -0.86 (0.38), residues: 176 loop : -1.74 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 646 TYR 0.012 0.002 TYR A 241 PHE 0.017 0.002 PHE A 325 TRP 0.013 0.001 TRP A 639 HIS 0.005 0.001 HIS A 903 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 7400) covalent geometry : angle 0.61488 / 0.32 (10263) hydrogen bonds : bond 0.04313 / 3.03 ( 320) hydrogen bonds : angle 5.76585 / 4.00 ( 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 141 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 99 time to evaluate : 0.241 Fit side-chains REVERT: A 327 ARG cc_start: 0.5290 (OUTLIER) cc_final: 0.4747 (mtt-85) REVERT: A 330 LYS cc_start: 0.6544 (OUTLIER) cc_final: 0.6184 (tptt) REVERT: A 348 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6829 (pmm) REVERT: A 503 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.5961 (pm20) REVERT: A 646 ARG cc_start: 0.5677 (mtm110) cc_final: 0.5390 (mtm110) REVERT: A 682 ILE cc_start: 0.6630 (OUTLIER) cc_final: 0.6335 (mp) REVERT: A 736 GLN cc_start: 0.6617 (OUTLIER) cc_final: 0.6324 (mm110) REVERT: A 801 ASN cc_start: 0.5488 (t0) cc_final: 0.5167 (t0) REVERT: A 845 MET cc_start: 0.8283 (ttt) cc_final: 0.7977 (ttt) outliers start: 42 outliers final: 21 residues processed: 128 average time/residue: 0.3883 time to fit residues: 53.2135 Evaluate side-chains 119 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 503 GLU 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 677 ASP Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 752 MET 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 52 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 56 optimal weight: 0.0000 chunk 66 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 HIS A 655 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.206569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.169398 restraints weight = 8334.506| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.46 r_work: 0.3994 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7400 Z= 0.128 Angle : 0.599 7.996 10263 Z= 0.314 Chirality : 0.043 0.151 1204 Planarity : 0.004 0.038 1111 Dihedral : 17.498 80.393 1580 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 6.00 % Allowed : 29.72 % Favored : 64.28 % 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 are not related in a simple way. whole: -1.43 (0.29), residues: 751 helix: 0.11 (0.33), residues: 221 sheet: -0.86 (0.37), residues: 176 loop : -1.65 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 652 TYR 0.008 0.001 TYR A 770 PHE 0.017 0.002 PHE A 341 TRP 0.010 0.001 TRP A 639 HIS 0.007 0.001 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 7400) covalent geometry : angle 0.59894 / 0.31 (10263) hydrogen bonds : bond 0.04132 / 2.89 ( 320) hydrogen bonds : angle 5.63323 / 3.90 ( 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 145 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 0.182 Fit side-chains REVERT: A 230 LYS cc_start: 0.2973 (OUTLIER) cc_final: 0.1624 (ptpp) REVERT: A 305 GLN cc_start: 0.7300 (tp40) cc_final: 0.6812 (tp40) REVERT: A 327 ARG cc_start: 0.5108 (OUTLIER) cc_final: 0.4599 (mtt-85) REVERT: A 330 LYS cc_start: 0.6497 (OUTLIER) cc_final: 0.6284 (tptt) REVERT: A 348 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6580 (pmm) REVERT: A 503 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.5808 (pm20) REVERT: A 579 VAL cc_start: 0.7705 (t) cc_final: 0.7358 (p) REVERT: A 682 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6499 (mp) REVERT: A 736 GLN cc_start: 0.6666 (OUTLIER) cc_final: 0.6416 (mm110) REVERT: A 777 MET cc_start: 0.2851 (mmp) cc_final: 0.2419 (mmt) REVERT: A 801 ASN cc_start: 0.5310 (t0) cc_final: 0.4852 (t0) REVERT: A 845 MET cc_start: 0.8222 (ttt) cc_final: 0.7934 (ttt) outliers start: 41 outliers final: 21 residues processed: 133 average time/residue: 0.3287 time to fit residues: 47.0258 Evaluate side-chains 119 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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 314 SER 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 349 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 429 ASP 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 568 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 682 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.201843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.164383 restraints weight = 8340.519| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 2.38 r_work: 0.3940 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3800 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7400 Z= 0.183 Angle : 0.658 8.193 10263 Z= 0.342 Chirality : 0.046 0.216 1204 Planarity : 0.005 0.042 1111 Dihedral : 17.431 80.201 1580 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 6.30 % Allowed : 31.19 % Favored : 62.52 % 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 are not related in a simple way. whole: -1.37 (0.29), residues: 751 helix: 0.21 (0.33), residues: 221 sheet: -0.87 (0.37), residues: 176 loop : -1.62 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 646 TYR 0.012 0.002 TYR A 888 PHE 0.019 0.002 PHE A 325 TRP 0.009 0.002 TRP A 639 HIS 0.005 0.001 HIS A 903 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 7400) covalent geometry : angle 0.65768 / 0.34 (10263) hydrogen bonds : bond 0.04352 / 3.05 ( 320) hydrogen bonds : angle 5.63543 / 3.89 ( 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 140 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 97 time to evaluate : 0.212 Fit side-chains REVERT: A 230 LYS cc_start: 0.3771 (OUTLIER) cc_final: 0.2141 (ptpp) REVERT: A 288 GLU cc_start: 0.7126 (mp0) cc_final: 0.6631 (tp30) REVERT: A 305 GLN cc_start: 0.7501 (tp40) cc_final: 0.6965 (tp40) REVERT: A 330 LYS cc_start: 0.6842 (OUTLIER) cc_final: 0.6562 (tttp) REVERT: A 348 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7001 (pmm) REVERT: A 503 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.5922 (pm20) REVERT: A 682 ILE cc_start: 0.6790 (OUTLIER) cc_final: 0.6451 (mp) REVERT: A 736 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6579 (mm110) REVERT: A 801 ASN cc_start: 0.5466 (t0) cc_final: 0.4885 (t0) REVERT: A 845 MET cc_start: 0.8469 (ttt) cc_final: 0.8120 (ttt) REVERT: A 868 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.7889 (t) REVERT: A 878 THR cc_start: 0.8375 (m) cc_final: 0.8117 (m) outliers start: 43 outliers final: 21 residues processed: 129 average time/residue: 0.3335 time to fit residues: 46.5502 Evaluate side-chains 117 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.150 ------------------------------------------------------------------------------- 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 314 SER Chi-restraints excluded: chain A residue 324 VAL 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 429 ASP 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 647 ILE Chi-restraints excluded: chain A residue 682 ILE 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 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: 8.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.207909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.172356 restraints weight = 8409.207| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 2.05 r_work: 0.4200 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4089 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 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 : 0.004 0.042 7400 Z= 0.195 Angle : 0.685 11.625 10263 Z= 0.353 Chirality : 0.046 0.180 1204 Planarity : 0.005 0.081 1111 Dihedral : 17.448 81.752 1580 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 6.30 % Allowed : 31.48 % 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 are not related in a simple way. whole: -1.39 (0.29), residues: 751 helix: 0.23 (0.33), residues: 220 sheet: -0.93 (0.37), residues: 176 loop : -1.63 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 646 TYR 0.012 0.002 TYR A 888 PHE 0.016 0.002 PHE A 325 TRP 0.011 0.002 TRP A 639 HIS 0.006 0.001 HIS A 903 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 ( 7400) covalent geometry : angle 0.68507 / 0.35 (10263) hydrogen bonds : bond 0.04372 / 3.06 ( 320) hydrogen bonds : angle 5.68239 / 3.91 ( 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 145 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 0.228 Fit side-chains REVERT: A 230 LYS cc_start: 0.4211 (OUTLIER) cc_final: 0.2738 (ptpp) REVERT: A 288 GLU cc_start: 0.6979 (mp0) cc_final: 0.6612 (tp30) REVERT: A 305 GLN cc_start: 0.7508 (tp40) cc_final: 0.6995 (tp40) REVERT: A 348 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6746 (pmm) REVERT: A 503 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5932 (pm20) REVERT: A 646 ARG cc_start: 0.5390 (mtm110) cc_final: 0.4942 (mtm110) REVERT: A 670 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7251 (mp) REVERT: A 682 ILE cc_start: 0.6908 (OUTLIER) cc_final: 0.6568 (mp) REVERT: A 736 GLN cc_start: 0.6922 (OUTLIER) cc_final: 0.6633 (mm110) REVERT: A 777 MET cc_start: 0.2977 (mmp) cc_final: 0.2467 (mmt) REVERT: A 801 ASN cc_start: 0.5380 (t0) cc_final: 0.4820 (t0) REVERT: A 845 MET cc_start: 0.8454 (ttt) cc_final: 0.8112 (ttt) REVERT: A 878 THR cc_start: 0.8428 (m) cc_final: 0.8171 (m) outliers start: 43 outliers final: 21 residues processed: 132 average time/residue: 0.3492 time to fit residues: 49.6586 Evaluate side-chains 123 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 314 SER 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 503 GLU Chi-restraints excluded: chain A residue 544 SER 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 682 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 45 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4559 r_free = 0.4559 target = 0.211466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.176888 restraints weight = 8483.711| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 2.05 r_work: 0.4251 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.4141 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.1958 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= 0.132 Angle : 0.634 12.311 10263 Z= 0.329 Chirality : 0.043 0.170 1204 Planarity : 0.004 0.042 1111 Dihedral : 17.480 83.153 1580 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.30), residues: 751 helix: 0.45 (0.34), residues: 220 sheet: -0.82 (0.38), residues: 170 loop : -1.52 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 564 TYR 0.009 0.001 TYR A 770 PHE 0.010 0.001 PHE A 497 TRP 0.012 0.001 TRP A 639 HIS 0.004 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 7400) covalent geometry : angle 0.63414 / 0.33 (10263) hydrogen bonds : bond 0.03985 / 2.82 ( 320) hydrogen bonds : angle 5.57548 / 3.84 ( 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: 33 poor density : 100 time to evaluate : 0.167 Fit side-chains REVERT: A 230 LYS cc_start: 0.4085 (OUTLIER) cc_final: 0.2430 (ptpp) REVERT: A 231 ILE cc_start: 0.2646 (OUTLIER) cc_final: 0.2143 (mt) REVERT: A 288 GLU cc_start: 0.6839 (mp0) cc_final: 0.6478 (tp30) REVERT: A 305 GLN cc_start: 0.7456 (tp40) cc_final: 0.6936 (tp40) REVERT: A 348 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6730 (pmm) REVERT: A 503 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.5852 (pm20) REVERT: A 646 ARG cc_start: 0.5476 (mtm110) cc_final: 0.5221 (mtm110) REVERT: A 682 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6555 (mp) REVERT: A 736 GLN cc_start: 0.6824 (OUTLIER) cc_final: 0.6537 (mm110) REVERT: A 777 MET cc_start: 0.3124 (mmp) cc_final: 0.2702 (mmt) REVERT: A 801 ASN cc_start: 0.5435 (t0) cc_final: 0.4873 (t0) REVERT: A 845 MET cc_start: 0.8378 (ttt) cc_final: 0.8060 (ttt) REVERT: A 878 THR cc_start: 0.8349 (m) cc_final: 0.8088 (m) outliers start: 33 outliers final: 16 residues processed: 120 average time/residue: 0.3362 time to fit residues: 43.5240 Evaluate side-chains 117 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 314 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 429 ASP 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 682 ILE 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.212781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.178394 restraints weight = 8507.144| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 2.04 r_work: 0.4258 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.4149 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7400 Z= 0.131 Angle : 0.641 11.788 10263 Z= 0.331 Chirality : 0.043 0.165 1204 Planarity : 0.004 0.041 1111 Dihedral : 17.414 82.461 1580 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.81 % Allowed : 35.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.30), residues: 751 helix: 0.62 (0.35), residues: 218 sheet: -0.74 (0.38), residues: 167 loop : -1.49 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 646 TYR 0.010 0.001 TYR A 770 PHE 0.022 0.002 PHE A 950 TRP 0.012 0.001 TRP A 639 HIS 0.012 0.001 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 7400) covalent geometry : angle 0.64129 / 0.33 (10263) hydrogen bonds : bond 0.03987 / 2.78 ( 320) hydrogen bonds : angle 5.52636 / 3.79 ( 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 124 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.146 Fit side-chains REVERT: A 230 LYS cc_start: 0.3900 (OUTLIER) cc_final: 0.2370 (ptpp) REVERT: A 305 GLN cc_start: 0.7424 (tp40) cc_final: 0.6928 (tp40) REVERT: A 348 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.6891 (pmm) REVERT: A 503 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.5848 (pm20) REVERT: A 599 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7173 (pt) REVERT: A 646 ARG cc_start: 0.5509 (mtm110) cc_final: 0.5298 (mtm110) REVERT: A 670 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7229 (mp) REVERT: A 682 ILE cc_start: 0.6881 (OUTLIER) cc_final: 0.6543 (mp) REVERT: A 736 GLN cc_start: 0.6800 (OUTLIER) cc_final: 0.6522 (mm110) REVERT: A 777 MET cc_start: 0.3209 (mmp) cc_final: 0.2889 (mmt) REVERT: A 801 ASN cc_start: 0.5595 (t0) cc_final: 0.5035 (t0) REVERT: A 845 MET cc_start: 0.8305 (ttt) cc_final: 0.7987 (ttt) REVERT: A 878 THR cc_start: 0.8344 (m) cc_final: 0.8083 (m) outliers start: 26 outliers final: 16 residues processed: 114 average time/residue: 0.3439 time to fit residues: 42.3029 Evaluate side-chains 117 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.153 ------------------------------------------------------------------------------- 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 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 503 GLU 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 670 ILE Chi-restraints excluded: chain A residue 682 ILE 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 74 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS A 746 HIS A 840 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.209739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.176078 restraints weight = 8407.661| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 1.96 r_work: 0.4235 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4128 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2093 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= 0.164 Angle : 0.674 11.480 10263 Z= 0.346 Chirality : 0.045 0.210 1204 Planarity : 0.004 0.043 1111 Dihedral : 17.387 81.620 1580 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.25 % Allowed : 34.99 % Favored : 60.76 % 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 are not related in a simple way. whole: -1.05 (0.30), residues: 751 helix: 0.51 (0.34), residues: 220 sheet: -0.73 (0.37), residues: 176 loop : -1.43 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 327 TYR 0.011 0.002 TYR A 888 PHE 0.021 0.002 PHE A 950 TRP 0.011 0.002 TRP A 639 HIS 0.005 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 7400) covalent geometry : angle 0.67367 / 0.35 (10263) hydrogen bonds : bond 0.04098 / 2.86 ( 320) hydrogen bonds : angle 5.52927 / 3.79 ( 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 124 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.177 Fit side-chains REVERT: A 230 LYS cc_start: 0.3981 (OUTLIER) cc_final: 0.2544 (ptpp) REVERT: A 254 MET cc_start: 0.5661 (pmm) cc_final: 0.5454 (pmt) REVERT: A 305 GLN cc_start: 0.7409 (tp40) cc_final: 0.6943 (tp40) REVERT: A 348 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6834 (pmm) REVERT: A 503 GLU cc_start: 0.6320 (OUTLIER) cc_final: 0.5842 (pm20) REVERT: A 599 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7241 (pt) REVERT: A 670 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7235 (mp) REVERT: A 682 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6493 (mp) REVERT: A 736 GLN cc_start: 0.6850 (OUTLIER) cc_final: 0.6589 (mm110) REVERT: A 801 ASN cc_start: 0.5610 (t0) cc_final: 0.5027 (t0) REVERT: A 845 MET cc_start: 0.8355 (ttt) cc_final: 0.7994 (ttt) REVERT: A 878 THR cc_start: 0.8348 (m) cc_final: 0.8113 (m) outliers start: 29 outliers final: 21 residues processed: 113 average time/residue: 0.3273 time to fit residues: 39.8845 Evaluate side-chains 117 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 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 429 ASP 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 682 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 752 MET 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 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: 1.9990 chunk 63 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 1 optimal weight: 0.0470 chunk 78 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4573 r_free = 0.4573 target = 0.212471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.178159 restraints weight = 8417.307| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 2.01 r_work: 0.4202 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4095 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7400 Z= 0.137 Angle : 0.663 11.527 10263 Z= 0.338 Chirality : 0.044 0.203 1204 Planarity : 0.004 0.041 1111 Dihedral : 17.390 82.292 1580 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.54 % Allowed : 35.14 % 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 are not related in a simple way. whole: -0.95 (0.30), residues: 751 helix: 0.58 (0.34), residues: 221 sheet: -0.74 (0.37), residues: 177 loop : -1.31 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 646 TYR 0.010 0.001 TYR A 770 PHE 0.021 0.002 PHE A 950 TRP 0.009 0.001 TRP A 884 HIS 0.005 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 7400) covalent geometry : angle 0.66258 / 0.34 (10263) hydrogen bonds : bond 0.03894 / 2.74 ( 320) hydrogen bonds : angle 5.47252 / 3.74 ( 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 131 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.224 Fit side-chains REVERT: A 230 LYS cc_start: 0.4053 (OUTLIER) cc_final: 0.2375 (ptpp) REVERT: A 305 GLN cc_start: 0.7501 (tp40) cc_final: 0.6995 (tp40) REVERT: A 348 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.6813 (pmm) REVERT: A 503 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.5901 (pm20) REVERT: A 599 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7278 (pt) REVERT: A 670 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7198 (mp) REVERT: A 682 ILE cc_start: 0.6740 (OUTLIER) cc_final: 0.6397 (mp) REVERT: A 736 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6506 (mm110) REVERT: A 777 MET cc_start: 0.2874 (mmp) cc_final: 0.2449 (mmt) REVERT: A 801 ASN cc_start: 0.5585 (t0) cc_final: 0.4995 (t0) REVERT: A 845 MET cc_start: 0.8341 (ttt) cc_final: 0.8011 (ttt) REVERT: A 878 THR cc_start: 0.8368 (m) cc_final: 0.8114 (m) outliers start: 31 outliers final: 20 residues processed: 119 average time/residue: 0.3366 time to fit residues: 43.1561 Evaluate side-chains 122 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 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 429 ASP 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 670 ILE Chi-restraints excluded: chain A residue 682 ILE 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 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: 0.8980 chunk 48 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.210367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.176842 restraints weight = 8387.188| |-----------------------------------------------------------------------------| r_work (start): 0.4320 rms_B_bonded: 1.96 r_work: 0.4245 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4138 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7400 Z= 0.159 Angle : 0.669 9.157 10263 Z= 0.342 Chirality : 0.045 0.198 1204 Planarity : 0.004 0.043 1111 Dihedral : 17.362 81.788 1580 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.83 % Allowed : 34.85 % 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 are not related in a simple way. whole: -1.00 (0.30), residues: 751 helix: 0.56 (0.34), residues: 217 sheet: -0.75 (0.36), residues: 182 loop : -1.35 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 646 TYR 0.010 0.002 TYR A 888 PHE 0.022 0.002 PHE A 950 TRP 0.015 0.002 TRP A 604 HIS 0.004 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 7400) covalent geometry : angle 0.66881 / 0.34 (10263) hydrogen bonds : bond 0.04013 / 2.81 ( 320) hydrogen bonds : angle 5.50168 / 3.76 ( 886) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2111.01 seconds wall clock time: 36 minutes 45.14 seconds (2205.14 seconds total)