Starting phenix.real_space_refine on Thu Jul 2 05:28:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij5_60616/07_2026/9ij5_60616.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij5_60616/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ij5_60616/07_2026/9ij5_60616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij5_60616/07_2026/9ij5_60616.map" model { file = "/net/cci-nas-00/data/ceres_data/9ij5_60616/07_2026/9ij5_60616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij5_60616/07_2026/9ij5_60616.cif" } 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-dev-6108/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: 1.35, 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: 0.44 Conformation dependent library (CDL) restraints added in 328.5 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: 0.77 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: 1.06 Time building geometry restraints manager: 0.59 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: 9934 2.91 - 5.82: 280 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: 1015 0.086 - 0.173: 175 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: 0.210 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: 7.820 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:7.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.760 ------------------------------------------------------------------------------- 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= 0.378 Angle : 1.162 14.538 10263 Z= 0.749 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 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 0.00758 / 0.38 ( 7400) covalent geometry : angle 1.16219 / 0.75 (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 : 0.259 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: 0.3786 time to fit residues: 42.7104 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 : 0.254 ------------------------------------------------------------------------------- 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 = 0.4525 r_free = 0.4525 target = 0.212087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.176750 restraints weight = 8512.995| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 2.16 r_work: 0.4174 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4063 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7400 Z= 0.135 Angle : 0.632 8.249 10263 Z= 0.337 Chirality : 0.044 0.180 1204 Planarity : 0.006 0.082 1111 Dihedral : 17.837 82.673 1590 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.69 % Allowed : 29.87 % Favored : 65.45 % 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: -2.05 (0.28), residues: 751 helix: -0.78 (0.31), residues: 221 sheet: -0.89 (0.38), residues: 176 loop : -1.95 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 652 TYR 0.013 0.001 TYR A 241 PHE 0.020 0.002 PHE A 325 TRP 0.016 0.001 TRP A 639 HIS 0.004 0.001 HIS A 903 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 7400) covalent geometry : angle 0.63227 / 0.34 (10263) hydrogen bonds : bond 0.04550 / 3.24 ( 320) hydrogen bonds : angle 6.05449 / 4.21 ( 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 129 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.197 Fit side-chains REVERT: A 348 MET cc_start: 0.7359 (pmm) cc_final: 0.7099 (pmm) REVERT: A 456 LYS cc_start: 0.6684 (OUTLIER) cc_final: 0.5303 (tptt) REVERT: A 512 MET cc_start: 0.7668 (mmm) cc_final: 0.7057 (tpp) REVERT: A 513 LYS cc_start: 0.6755 (tttm) cc_final: 0.6042 (ttpm) REVERT: A 736 GLN cc_start: 0.6525 (OUTLIER) cc_final: 0.6257 (mm110) REVERT: A 773 VAL cc_start: 0.7190 (OUTLIER) cc_final: 0.6957 (p) REVERT: A 777 MET cc_start: 0.3087 (mmp) cc_final: 0.2729 (mmt) REVERT: A 801 ASN cc_start: 0.5202 (t0) cc_final: 0.4607 (t0) REVERT: A 845 MET cc_start: 0.8428 (ttt) cc_final: 0.8132 (ttt) outliers start: 32 outliers final: 9 residues processed: 118 average time/residue: 0.3869 time to fit residues: 49.1185 Evaluate side-chains 102 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 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 744 VAL 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: 0.0870 chunk 35 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.4540 r_free = 0.4540 target = 0.213487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.178405 restraints weight = 8351.024| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 2.12 r_work: 0.4195 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4084 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7400 Z= 0.115 Angle : 0.587 7.315 10263 Z= 0.311 Chirality : 0.043 0.175 1204 Planarity : 0.005 0.043 1111 Dihedral : 17.652 81.712 1580 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 5.27 % Allowed : 30.31 % Favored : 64.42 % 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: -0.28 (0.32), residues: 222 sheet: -0.79 (0.38), residues: 176 loop : -1.76 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 652 TYR 0.012 0.001 TYR A 241 PHE 0.015 0.002 PHE A 325 TRP 0.013 0.001 TRP A 639 HIS 0.003 0.001 HIS A 903 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 7400) covalent geometry : angle 0.58656 / 0.31 (10263) hydrogen bonds : bond 0.04237 / 2.99 ( 320) hydrogen bonds : angle 5.73247 / 3.98 ( 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 134 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.233 Fit side-chains REVERT: A 327 ARG cc_start: 0.5224 (OUTLIER) cc_final: 0.4700 (mtt-85) REVERT: A 330 LYS cc_start: 0.6407 (OUTLIER) cc_final: 0.6142 (tptt) REVERT: A 348 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6736 (pmm) REVERT: A 456 LYS cc_start: 0.6721 (OUTLIER) cc_final: 0.5326 (tptt) REVERT: A 646 ARG cc_start: 0.5609 (mtm110) cc_final: 0.5086 (mtm110) REVERT: A 736 GLN cc_start: 0.6516 (OUTLIER) cc_final: 0.6226 (mm110) REVERT: A 801 ASN cc_start: 0.5446 (t0) cc_final: 0.5147 (t0) REVERT: A 845 MET cc_start: 0.8179 (ttt) cc_final: 0.7836 (ttt) outliers start: 36 outliers final: 15 residues processed: 123 average time/residue: 0.4215 time to fit residues: 55.4543 Evaluate side-chains 111 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE 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 424 THR Chi-restraints excluded: chain A residue 456 LYS 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 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 875 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 935 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 52 optimal weight: 7.9990 chunk 69 optimal weight: 0.0670 chunk 61 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 64 optimal weight: 0.2980 chunk 32 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 HIS ** A 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.208857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.172689 restraints weight = 8361.897| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 2.10 r_work: 0.4038 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3899 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7400 Z= 0.116 Angle : 0.583 7.307 10263 Z= 0.309 Chirality : 0.043 0.179 1204 Planarity : 0.004 0.038 1111 Dihedral : 17.588 82.008 1580 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.71 % Allowed : 29.28 % 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 are not related in a simple way. whole: -1.38 (0.29), residues: 751 helix: 0.09 (0.33), residues: 221 sheet: -0.75 (0.37), residues: 176 loop : -1.63 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 646 TYR 0.011 0.001 TYR A 241 PHE 0.015 0.001 PHE A 341 TRP 0.011 0.001 TRP A 639 HIS 0.005 0.001 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 7400) covalent geometry : angle 0.58327 / 0.31 (10263) hydrogen bonds : bond 0.04077 / 2.84 ( 320) hydrogen bonds : angle 5.63469 / 3.92 ( 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 139 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 0.176 Fit side-chains REVERT: A 230 LYS cc_start: 0.3160 (OUTLIER) cc_final: 0.1740 (ptpp) REVERT: A 290 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7614 (mmpt) REVERT: A 327 ARG cc_start: 0.5255 (OUTLIER) cc_final: 0.4785 (mtt-85) REVERT: A 348 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.6776 (pmm) REVERT: A 456 LYS cc_start: 0.6778 (OUTLIER) cc_final: 0.5414 (tptt) REVERT: A 503 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5823 (pm20) REVERT: A 736 GLN cc_start: 0.6634 (OUTLIER) cc_final: 0.6379 (mm110) REVERT: A 777 MET cc_start: 0.2701 (mmp) cc_final: 0.2373 (mmt) REVERT: A 801 ASN cc_start: 0.5386 (t0) cc_final: 0.4858 (t0) REVERT: A 845 MET cc_start: 0.8263 (ttt) cc_final: 0.8026 (ttt) outliers start: 39 outliers final: 18 residues processed: 129 average time/residue: 0.3565 time to fit residues: 49.2994 Evaluate side-chains 113 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 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 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 334 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 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 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 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: 0.0670 chunk 0 optimal weight: 30.0000 chunk 10 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 overall best weight: 2.7924 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.200646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.163184 restraints weight = 8325.957| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 2.06 r_work: 0.3934 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7400 Z= 0.221 Angle : 0.684 7.933 10263 Z= 0.357 Chirality : 0.047 0.207 1204 Planarity : 0.005 0.043 1111 Dihedral : 17.501 80.957 1580 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 6.59 % Allowed : 31.19 % 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: -1.45 (0.29), residues: 751 helix: 0.05 (0.33), residues: 221 sheet: -0.80 (0.38), residues: 174 loop : -1.67 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 366 TYR 0.015 0.002 TYR A 361 PHE 0.020 0.003 PHE A 325 TRP 0.009 0.002 TRP A 932 HIS 0.006 0.001 HIS A 903 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 ( 7400) covalent geometry : angle 0.68356 / 0.36 (10263) hydrogen bonds : bond 0.04671 / 3.28 ( 320) hydrogen bonds : angle 5.72398 / 3.95 ( 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 145 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 100 time to evaluate : 0.204 Fit side-chains REVERT: A 230 LYS cc_start: 0.3824 (OUTLIER) cc_final: 0.2212 (ptpp) REVERT: A 288 GLU cc_start: 0.7237 (mp0) cc_final: 0.6568 (mm-30) REVERT: A 305 GLN cc_start: 0.7434 (tp40) cc_final: 0.6882 (tp40) REVERT: A 348 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7049 (pmm) REVERT: A 503 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.5971 (pm20) REVERT: A 682 ILE cc_start: 0.6909 (OUTLIER) cc_final: 0.6596 (mp) REVERT: A 736 GLN cc_start: 0.6881 (OUTLIER) cc_final: 0.6613 (mm110) REVERT: A 801 ASN cc_start: 0.5461 (t0) cc_final: 0.4877 (t0) REVERT: A 845 MET cc_start: 0.8491 (ttt) cc_final: 0.8092 (ttt) REVERT: A 878 THR cc_start: 0.8401 (m) cc_final: 0.8135 (m) outliers start: 45 outliers final: 21 residues processed: 136 average time/residue: 0.3863 time to fit residues: 56.3600 Evaluate side-chains 118 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 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 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: 7.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 0.0070 chunk 48 optimal weight: 0.0050 chunk 75 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 overall best weight: 0.4612 ------------------------------------------------------------------------------- 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 = 0.4431 r_free = 0.4431 target = 0.206424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.169937 restraints weight = 8249.105| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.09 r_work: 0.4013 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3873 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.1808 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= 0.122 Angle : 0.615 10.136 10263 Z= 0.321 Chirality : 0.043 0.167 1204 Planarity : 0.004 0.052 1111 Dihedral : 17.553 84.308 1580 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 5.27 % Allowed : 33.24 % Favored : 61.49 % 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: -1.19 (0.30), residues: 751 helix: 0.38 (0.34), residues: 221 sheet: -0.81 (0.38), residues: 172 loop : -1.51 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 646 TYR 0.009 0.001 TYR A 770 PHE 0.014 0.002 PHE A 838 TRP 0.010 0.001 TRP A 639 HIS 0.004 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 7400) covalent geometry : angle 0.61483 / 0.32 (10263) hydrogen bonds : bond 0.03937 / 2.77 ( 320) hydrogen bonds : angle 5.55770 / 3.83 ( 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 130 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.244 Fit side-chains REVERT: A 230 LYS cc_start: 0.3619 (OUTLIER) cc_final: 0.2047 (ptpp) REVERT: A 288 GLU cc_start: 0.7147 (mp0) cc_final: 0.6495 (mm-30) REVERT: A 290 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7689 (mmpt) REVERT: A 305 GLN cc_start: 0.7576 (tp40) cc_final: 0.7049 (tp40) REVERT: A 333 ASP cc_start: 0.7874 (t0) cc_final: 0.6909 (t0) REVERT: A 348 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.6789 (pmm) REVERT: A 503 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.5870 (pm20) REVERT: A 736 GLN cc_start: 0.6780 (OUTLIER) cc_final: 0.6510 (mm110) REVERT: A 777 MET cc_start: 0.2730 (mmp) cc_final: 0.2269 (mmt) REVERT: A 801 ASN cc_start: 0.5348 (t0) cc_final: 0.4753 (t0) REVERT: A 845 MET cc_start: 0.8343 (ttt) cc_final: 0.8007 (ttt) REVERT: A 878 THR cc_start: 0.8346 (m) cc_final: 0.8084 (m) outliers start: 36 outliers final: 21 residues processed: 120 average time/residue: 0.3945 time to fit residues: 50.9952 Evaluate side-chains 119 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 568 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 647 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 868 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 935 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 45 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS A 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.202640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.165614 restraints weight = 8286.036| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 2.09 r_work: 0.3966 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3827 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7400 Z= 0.169 Angle : 0.652 11.720 10263 Z= 0.340 Chirality : 0.045 0.208 1204 Planarity : 0.004 0.042 1111 Dihedral : 17.450 82.933 1580 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.83 % Allowed : 33.97 % Favored : 61.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.22 (0.30), residues: 751 helix: 0.36 (0.34), residues: 221 sheet: -0.86 (0.37), residues: 178 loop : -1.50 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.010 0.002 TYR A 888 PHE 0.020 0.002 PHE A 950 TRP 0.010 0.002 TRP A 639 HIS 0.008 0.001 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 7400) covalent geometry : angle 0.65194 / 0.34 (10263) hydrogen bonds : bond 0.04169 / 2.89 ( 320) hydrogen bonds : angle 5.56383 / 3.83 ( 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 135 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.242 Fit side-chains REVERT: A 230 LYS cc_start: 0.3964 (OUTLIER) cc_final: 0.2156 (ptpp) REVERT: A 254 MET cc_start: 0.5680 (pmm) cc_final: 0.5369 (pmt) REVERT: A 288 GLU cc_start: 0.7180 (mp0) cc_final: 0.6669 (tp30) REVERT: A 305 GLN cc_start: 0.7631 (tp40) cc_final: 0.7100 (tp40) REVERT: A 348 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7004 (pmm) REVERT: A 503 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.5957 (pm20) REVERT: A 646 ARG cc_start: 0.5364 (mtm110) cc_final: 0.5144 (mtm110) REVERT: A 670 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7173 (mp) REVERT: A 682 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6692 (mp) REVERT: A 736 GLN cc_start: 0.6856 (OUTLIER) cc_final: 0.6573 (mm110) REVERT: A 777 MET cc_start: 0.2801 (mmp) cc_final: 0.2344 (mmt) REVERT: A 801 ASN cc_start: 0.5416 (t0) cc_final: 0.4792 (t0) REVERT: A 845 MET cc_start: 0.8386 (ttt) cc_final: 0.7982 (ttt) REVERT: A 878 THR cc_start: 0.8321 (m) cc_final: 0.8050 (m) outliers start: 33 outliers final: 22 residues processed: 124 average time/residue: 0.3669 time to fit residues: 48.9611 Evaluate side-chains 122 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 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 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 752 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 44 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 64 optimal weight: 0.0020 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 0.0060 chunk 58 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.9408 ------------------------------------------------------------------------------- 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 A 422 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.205403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.168784 restraints weight = 8366.609| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.10 r_work: 0.3999 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3859 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.1956 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= 0.136 Angle : 0.641 10.757 10263 Z= 0.332 Chirality : 0.044 0.206 1204 Planarity : 0.004 0.042 1111 Dihedral : 17.471 83.926 1580 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.83 % Allowed : 33.82 % 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 are not related in a simple way. whole: -1.14 (0.30), residues: 751 helix: 0.48 (0.34), residues: 219 sheet: -0.83 (0.37), residues: 178 loop : -1.48 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 646 TYR 0.009 0.001 TYR A 770 PHE 0.018 0.002 PHE A 887 TRP 0.011 0.001 TRP A 639 HIS 0.005 0.001 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 7400) covalent geometry : angle 0.64132 / 0.33 (10263) hydrogen bonds : bond 0.03910 / 2.73 ( 320) hydrogen bonds : angle 5.51823 / 3.80 ( 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 129 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 time to evaluate : 0.152 Fit side-chains REVERT: A 230 LYS cc_start: 0.3891 (OUTLIER) cc_final: 0.2091 (ptpp) REVERT: A 288 GLU cc_start: 0.7072 (mp0) cc_final: 0.6460 (tp30) REVERT: A 290 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7748 (mmpt) REVERT: A 305 GLN cc_start: 0.7597 (tp40) cc_final: 0.7059 (tp40) REVERT: A 348 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6773 (pmm) REVERT: A 503 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5916 (pm20) REVERT: A 682 ILE cc_start: 0.6962 (OUTLIER) cc_final: 0.6659 (mp) REVERT: A 736 GLN cc_start: 0.6829 (OUTLIER) cc_final: 0.6546 (mm110) REVERT: A 777 MET cc_start: 0.2937 (mmp) cc_final: 0.2576 (mmt) REVERT: A 801 ASN cc_start: 0.5602 (t0) cc_final: 0.5022 (t0) REVERT: A 845 MET cc_start: 0.8340 (ttt) cc_final: 0.7965 (ttt) REVERT: A 878 THR cc_start: 0.8339 (m) cc_final: 0.8059 (m) outliers start: 33 outliers final: 22 residues processed: 119 average time/residue: 0.3976 time to fit residues: 50.9339 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 : 0.245 ------------------------------------------------------------------------------- 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 348 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 422 ASN 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 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 752 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 74 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.208611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.173339 restraints weight = 8418.104| |-----------------------------------------------------------------------------| r_work (start): 0.4291 rms_B_bonded: 2.03 r_work: 0.4206 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4096 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7400 Z= 0.215 Angle : 0.713 12.085 10263 Z= 0.365 Chirality : 0.047 0.190 1204 Planarity : 0.005 0.044 1111 Dihedral : 17.405 82.933 1580 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.12 % Allowed : 33.67 % Favored : 61.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.23 (0.29), residues: 751 helix: 0.40 (0.33), residues: 218 sheet: -0.82 (0.37), residues: 176 loop : -1.55 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 646 TYR 0.019 0.002 TYR A 420 PHE 0.026 0.003 PHE A 950 TRP 0.011 0.002 TRP A 639 HIS 0.007 0.001 HIS A 903 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 ( 7400) covalent geometry : angle 0.71263 / 0.37 (10263) hydrogen bonds : bond 0.04320 / 3.01 ( 320) hydrogen bonds : angle 5.57792 / 3.83 ( 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 127 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.249 Fit side-chains REVERT: A 230 LYS cc_start: 0.4083 (OUTLIER) cc_final: 0.2385 (ptpp) REVERT: A 254 MET cc_start: 0.5777 (pmm) cc_final: 0.5406 (pmt) REVERT: A 290 LYS cc_start: 0.7962 (mmtt) cc_final: 0.7653 (mmpt) REVERT: A 305 GLN cc_start: 0.7613 (tp40) cc_final: 0.7129 (tp40) REVERT: A 348 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6882 (pmm) REVERT: A 503 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.5954 (pm20) REVERT: A 670 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7215 (mp) REVERT: A 682 ILE cc_start: 0.7005 (OUTLIER) cc_final: 0.6758 (mp) REVERT: A 736 GLN cc_start: 0.6873 (OUTLIER) cc_final: 0.6561 (mm110) REVERT: A 801 ASN cc_start: 0.5634 (t0) cc_final: 0.5074 (t0) REVERT: A 845 MET cc_start: 0.8370 (ttt) cc_final: 0.8011 (ttt) REVERT: A 878 THR cc_start: 0.8369 (m) cc_final: 0.8102 (m) REVERT: A 928 MET cc_start: 0.8278 (tpt) cc_final: 0.8004 (tpt) outliers start: 35 outliers final: 21 residues processed: 116 average time/residue: 0.3898 time to fit residues: 48.8754 Evaluate side-chains 116 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 63 optimal weight: 6.9990 chunk 4 optimal weight: 0.0970 chunk 68 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 = 0.210495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.175730 restraints weight = 8453.346| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 2.03 r_work: 0.4234 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.4125 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.2068 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= 0.156 Angle : 0.685 9.500 10263 Z= 0.351 Chirality : 0.045 0.199 1204 Planarity : 0.004 0.042 1111 Dihedral : 17.440 84.445 1580 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.54 % Allowed : 34.55 % Favored : 60.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.13 (0.30), residues: 751 helix: 0.56 (0.34), residues: 217 sheet: -0.83 (0.36), residues: 176 loop : -1.51 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 646 TYR 0.011 0.002 TYR A 420 PHE 0.020 0.002 PHE A 950 TRP 0.012 0.001 TRP A 639 HIS 0.005 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 7400) covalent geometry : angle 0.68466 / 0.35 (10263) hydrogen bonds : bond 0.03960 / 2.76 ( 320) hydrogen bonds : angle 5.58573 / 3.84 ( 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 127 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.212 Fit side-chains REVERT: A 230 LYS cc_start: 0.3778 (OUTLIER) cc_final: 0.2062 (ptpp) REVERT: A 254 MET cc_start: 0.5727 (pmm) cc_final: 0.5409 (pmt) REVERT: A 288 GLU cc_start: 0.7186 (mp0) cc_final: 0.6859 (tp30) REVERT: A 290 LYS cc_start: 0.7911 (mmtt) cc_final: 0.7678 (mmpt) REVERT: A 305 GLN cc_start: 0.7583 (tp40) cc_final: 0.7127 (tp40) REVERT: A 348 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.6813 (pmm) REVERT: A 503 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.6054 (pm20) REVERT: A 670 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7215 (mp) REVERT: A 682 ILE cc_start: 0.7067 (OUTLIER) cc_final: 0.6791 (mp) REVERT: A 736 GLN cc_start: 0.6849 (OUTLIER) cc_final: 0.6533 (mm110) REVERT: A 777 MET cc_start: 0.2877 (mmp) cc_final: 0.2443 (mmt) REVERT: A 801 ASN cc_start: 0.5587 (t0) cc_final: 0.5035 (t0) REVERT: A 845 MET cc_start: 0.8317 (ttt) cc_final: 0.7978 (ttt) REVERT: A 878 THR cc_start: 0.8296 (m) cc_final: 0.8042 (m) REVERT: A 928 MET cc_start: 0.8157 (tpt) cc_final: 0.7837 (tpt) outliers start: 31 outliers final: 20 residues processed: 117 average time/residue: 0.3601 time to fit residues: 45.4390 Evaluate side-chains 118 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 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 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 22 optimal weight: 0.7980 chunk 48 optimal weight: 0.2980 chunk 57 optimal weight: 0.0770 chunk 45 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.4433 r_free = 0.4433 target = 0.206642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.170830 restraints weight = 8289.141| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 2.03 r_work: 0.4027 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3891 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7400 Z= 0.125 Angle : 0.647 9.128 10263 Z= 0.332 Chirality : 0.044 0.191 1204 Planarity : 0.004 0.041 1111 Dihedral : 17.429 84.536 1580 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.66 % Allowed : 35.58 % 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: -1.02 (0.30), residues: 751 helix: 0.68 (0.35), residues: 218 sheet: -0.73 (0.37), residues: 173 loop : -1.48 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 646 TYR 0.009 0.001 TYR A 420 PHE 0.021 0.002 PHE A 950 TRP 0.016 0.002 TRP A 604 HIS 0.006 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 7400) covalent geometry : angle 0.64721 / 0.33 (10263) hydrogen bonds : bond 0.03849 / 2.70 ( 320) hydrogen bonds : angle 5.47509 / 3.75 ( 886) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2389.09 seconds wall clock time: 41 minutes 35.29 seconds (2495.29 seconds total)