Starting phenix.real_space_refine on Tue Aug 4 21:26:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij1_60612/08_2026/9ij1_60612.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij1_60612/08_2026/9ij1_60612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ij1_60612/08_2026/9ij1_60612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij1_60612/08_2026/9ij1_60612.map" model { file = "/net/cci-nas-00/data/ceres_data/9ij1_60612/08_2026/9ij1_60612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij1_60612/08_2026/9ij1_60612.cif" } resolution = 3.2 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= 0.001 sd= 0.034 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 47 5.49 5 Mg 1 5.21 5 S 44 5.16 5 C 4328 2.51 5 N 1221 2.21 5 O 1415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s 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: 7056 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6062 Classifications: {'peptide': 755} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 717} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 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': 1, 'rna2p_pyr': 3, 'rna3p_pur': 12, 'rna3p_pyr': 10} Link IDs: {'rna2p': 3, 'rna3p': 22} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 443 Classifications: {'RNA': 21} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna3p': 20} 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: 1.79, per 1000 atoms: 0.25 Number of scatterers: 7056 At special positions: 0 Unit cell: (80.94, 86.64, 103.74, 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 47 15.00 Mg 1 11.99 O 1415 8.00 N 1221 7.00 C 4328 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: 0.41 Conformation dependent library (CDL) restraints added in 343.5 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: 24 helices and 12 sheets defined 31.1% alpha, 17.4% beta 20 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 251 through 261 removed outlier: 3.658A pdb=" N ARG A 255 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) 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 330 removed outlier: 3.559A pdb=" N PHE A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 399 Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 502 through 507 removed outlier: 3.861A pdb=" N LYS A 507 " --> pdb=" O GLU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 520 removed outlier: 4.894A pdb=" N GLN A 517 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLN A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A 519 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 539 Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.609A pdb=" N GLU A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 590 removed outlier: 4.109A pdb=" N VAL A 590 " --> pdb=" O VAL A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 624 removed outlier: 3.662A pdb=" N LEU A 619 " --> pdb=" O GLN A 615 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASN A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N MET A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 649 through 658 removed outlier: 4.213A pdb=" N ILE A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN A 655 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 664 removed outlier: 4.196A pdb=" N LYS A 663 " --> pdb=" O VAL A 660 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 664 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 689 removed outlier: 3.673A pdb=" N TYR A 679 " --> pdb=" O ARG A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 723 Processing helix chain 'A' and resid 785 through 801 Processing helix chain 'A' and resid 819 through 826 Processing helix chain 'A' and resid 827 through 835 removed outlier: 3.924A pdb=" N PHE A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) 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 914 through 927 Processing helix chain 'A' and resid 939 through 955 removed outlier: 3.594A pdb=" N HIS A 946 " --> pdb=" O CYS A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 965 Processing sheet with id=AA1, first strand: chain 'A' and resid 271 through 272 removed outlier: 3.727A pdb=" N ALA A 271 " --> pdb=" O TYR A 278 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL A 238 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE A 309 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLN A 240 " --> pdb=" O THR A 307 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 242 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN A 305 " --> pdb=" O HIS A 242 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 350 removed outlier: 7.766A pdb=" N ASP A 386 " --> pdb=" O MET A 498 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET A 498 " --> pdb=" O ASP A 386 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 499 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE A 415 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 362 through 368 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 577 through 579 Processing sheet with id=AA8, first strand: chain 'A' and resid 605 through 608 removed outlier: 3.783A pdb=" N TYR A 608 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 668 through 671 removed outlier: 6.219A pdb=" N CYS A 669 " --> pdb=" O ILE A 697 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 737 through 740 removed outlier: 7.755A pdb=" N MET A 845 " --> pdb=" O ASN A 909 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN A 909 " --> pdb=" O MET A 845 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 847 " --> pdb=" O VAL A 907 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL A 885 " --> pdb=" O CYS A 906 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 743 through 745 removed outlier: 4.048A pdb=" N VAL A 756 " --> pdb=" O VAL A 774 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 774 " --> pdb=" O VAL A 756 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 860 through 861 208 hydrogen bonds defined for protein. 567 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2077 1.34 - 1.46: 1889 1.46 - 1.59: 3179 1.59 - 1.71: 92 1.71 - 1.83: 69 Bond restraints: 7306 Sorted by residual: bond pdb=" N9 A B 6 " pdb=" C4 A B 6 " ideal model delta sigma weight residual 1.374 1.393 -0.019 6.00e-03 2.78e+04 9.69e+00 bond pdb=" C8 A B 6 " pdb=" N7 A B 6 " ideal model delta sigma weight residual 1.311 1.296 0.015 7.00e-03 2.04e+04 4.30e+00 bond pdb=" N7 A B 6 " pdb=" C5 A B 6 " ideal model delta sigma weight residual 1.388 1.376 0.012 6.00e-03 2.78e+04 4.29e+00 bond pdb=" C4 C B 11 " pdb=" C5 C B 11 " ideal model delta sigma weight residual 1.425 1.409 0.016 8.00e-03 1.56e+04 3.76e+00 bond pdb=" CB VAL A 388 " pdb=" CG2 VAL A 388 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.37e+00 ... (remaining 7301 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 9843 2.78 - 5.55: 213 5.55 - 8.33: 34 8.33 - 11.11: 17 11.11 - 13.88: 7 Bond angle restraints: 10114 Sorted by residual: angle pdb=" N1 C B 11 " pdb=" C6 C B 11 " pdb=" C5 C B 11 " ideal model delta sigma weight residual 121.00 124.73 -3.73 5.00e-01 4.00e+00 5.56e+01 angle pdb=" O5' U B 2 " pdb=" C5' U B 2 " pdb=" C4' U B 2 " ideal model delta sigma weight residual 109.40 114.35 -4.95 8.00e-01 1.56e+00 3.82e+01 angle pdb=" C3' U B 1 " pdb=" O3' U B 1 " pdb=" P U B 2 " ideal model delta sigma weight residual 119.70 126.91 -7.21 1.20e+00 6.94e-01 3.61e+01 angle pdb=" C2 C B 11 " pdb=" N1 C B 11 " pdb=" C6 C B 11 " ideal model delta sigma weight residual 120.30 117.92 2.38 4.00e-01 6.25e+00 3.53e+01 angle pdb=" CA MET A 613 " pdb=" CB MET A 613 " pdb=" CG MET A 613 " ideal model delta sigma weight residual 114.10 125.50 -11.40 2.00e+00 2.50e-01 3.25e+01 ... (remaining 10109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.72: 4052 29.72 - 59.44: 357 59.44 - 89.17: 49 89.17 - 118.89: 2 118.89 - 148.61: 2 Dihedral angle restraints: 4462 sinusoidal: 2252 harmonic: 2210 Sorted by residual: dihedral pdb=" CA MET A 498 " pdb=" C MET A 498 " pdb=" N THR A 499 " pdb=" CA THR A 499 " ideal model delta harmonic sigma weight residual 180.00 144.46 35.54 0 5.00e+00 4.00e-02 5.05e+01 dihedral pdb=" CA LEU A 727 " pdb=" C LEU A 727 " pdb=" N TRP A 728 " pdb=" CA TRP A 728 " ideal model delta harmonic sigma weight residual 180.00 150.53 29.47 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ILE A 626 " pdb=" C ILE A 626 " pdb=" N ALA A 627 " pdb=" CA ALA A 627 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 4459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 856 0.060 - 0.120: 239 0.120 - 0.180: 79 0.180 - 0.240: 5 0.240 - 0.300: 3 Chirality restraints: 1182 Sorted by residual: chirality pdb=" C3' G C 12 " pdb=" C4' G C 12 " pdb=" O3' G C 12 " pdb=" C2' G C 12 " both_signs ideal model delta sigma weight residual False -2.48 -2.18 -0.30 2.00e-01 2.50e+01 2.25e+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 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" P U B 2 " pdb=" OP1 U B 2 " pdb=" OP2 U B 2 " pdb=" O5' U B 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.66 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1179 not shown) Planarity restraints: 1110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 435 " -0.056 5.00e-02 4.00e+02 8.50e-02 1.16e+01 pdb=" N PRO A 436 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 436 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 436 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 492 " -0.055 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO A 493 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 493 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 493 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 938 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO A 939 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 939 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 939 " 0.039 5.00e-02 4.00e+02 ... (remaining 1107 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 154 2.66 - 3.22: 5766 3.22 - 3.78: 12023 3.78 - 4.34: 15296 4.34 - 4.90: 23707 Nonbonded interactions: 56946 Sorted by model distance: nonbonded pdb=" OP1 U C 13 " pdb="MG MG A1001 " model vdw 2.099 2.170 nonbonded pdb=" OD2 ASP A 273 " pdb=" O2' U C 7 " model vdw 2.260 3.040 nonbonded pdb=" OP2 U C 13 " pdb="MG MG A1001 " model vdw 2.330 2.170 nonbonded pdb=" OG SER A 581 " pdb=" OD1 ASP A 583 " model vdw 2.331 3.040 nonbonded pdb=" O HIS A 602 " pdb=" OG SER A 635 " model vdw 2.336 3.040 ... (remaining 56941 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: 0.290 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.960 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 7306 Z= 0.262 Angle : 1.117 13.884 10114 Z= 0.697 Chirality : 0.062 0.300 1182 Planarity : 0.009 0.085 1110 Dihedral : 20.534 148.611 3032 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.88 % Allowed : 36.31 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.66 (0.28), residues: 751 helix: -2.19 (0.31), residues: 194 sheet: -0.59 (0.41), residues: 149 loop : -2.01 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 772 TYR 0.028 0.003 TYR A 453 PHE 0.024 0.003 PHE A 578 TRP 0.021 0.002 TRP A 728 HIS 0.011 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.26 ( 7306) covalent geometry : angle 1.11694 / 0.70 (10114) hydrogen bonds : bond 0.14185 / 9.78 ( 256) hydrogen bonds : angle 7.18849 / 5.03 ( 663) *********************** 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 107 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 THR cc_start: 0.5535 (t) cc_final: 0.5107 (t) REVERT: A 947 LYS cc_start: 0.6192 (mmmt) cc_final: 0.5644 (mmtt) outliers start: 6 outliers final: 3 residues processed: 104 average time/residue: 0.0765 time to fit residues: 11.2275 Evaluate side-chains 94 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 931 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 380 HIS A 422 ASN A 472 HIS ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5152 r_free = 0.5152 target = 0.293177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5039 r_free = 0.5039 target = 0.252753 restraints weight = 10698.918| |-----------------------------------------------------------------------------| r_work (start): 0.4784 rms_B_bonded: 2.58 r_work: 0.4653 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6171 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7306 Z= 0.208 Angle : 0.749 8.895 10114 Z= 0.392 Chirality : 0.051 0.262 1182 Planarity : 0.007 0.064 1110 Dihedral : 18.024 157.942 1524 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 6.00 % Allowed : 32.65 % Favored : 61.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.53 (0.29), residues: 751 helix: -1.69 (0.34), residues: 204 sheet: -0.64 (0.43), residues: 149 loop : -2.11 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 652 TYR 0.024 0.002 TYR A 859 PHE 0.030 0.003 PHE A 887 TRP 0.017 0.002 TRP A 728 HIS 0.007 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 ( 7306) covalent geometry : angle 0.74858 / 0.39 (10114) hydrogen bonds : bond 0.06331 / 4.44 ( 256) hydrogen bonds : angle 5.90972 / 4.11 ( 663) *********************** 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 133 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 302 ILE cc_start: 0.5626 (OUTLIER) cc_final: 0.5327 (mp) REVERT: A 321 TYR cc_start: 0.6445 (m-10) cc_final: 0.5727 (m-10) REVERT: A 548 THR cc_start: 0.5686 (t) cc_final: 0.5219 (t) REVERT: A 623 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6374 (mm) REVERT: A 799 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6405 (tm-30) REVERT: A 889 LEU cc_start: 0.5730 (OUTLIER) cc_final: 0.5489 (mp) REVERT: A 947 LYS cc_start: 0.6720 (mmmt) cc_final: 0.6128 (mmtt) outliers start: 41 outliers final: 24 residues processed: 123 average time/residue: 0.0714 time to fit residues: 12.6619 Evaluate side-chains 116 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 970 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 7.9990 chunk 71 optimal weight: 0.0030 chunk 36 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 8 optimal weight: 0.3980 chunk 48 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 713 GLN ** A 896 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 = 0.5188 r_free = 0.5188 target = 0.297715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.5083 r_free = 0.5083 target = 0.258104 restraints weight = 10531.541| |-----------------------------------------------------------------------------| r_work (start): 0.4819 rms_B_bonded: 2.63 r_work: 0.4692 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7306 Z= 0.122 Angle : 0.647 8.987 10114 Z= 0.337 Chirality : 0.046 0.236 1182 Planarity : 0.006 0.062 1110 Dihedral : 17.962 156.913 1524 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 6.30 % Allowed : 32.36 % 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: -2.28 (0.29), residues: 751 helix: -1.40 (0.35), residues: 204 sheet: -0.47 (0.44), residues: 149 loop : -2.01 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 366 TYR 0.017 0.002 TYR A 944 PHE 0.022 0.002 PHE A 887 TRP 0.017 0.001 TRP A 728 HIS 0.006 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 7306) covalent geometry : angle 0.64686 / 0.34 (10114) hydrogen bonds : bond 0.05597 / 3.95 ( 256) hydrogen bonds : angle 5.68439 / 4.02 ( 663) *********************** 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 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 91 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 ILE cc_start: 0.5537 (OUTLIER) cc_final: 0.5237 (mp) REVERT: A 320 PHE cc_start: 0.4299 (OUTLIER) cc_final: 0.3563 (p90) REVERT: A 321 TYR cc_start: 0.6284 (m-10) cc_final: 0.5535 (m-10) REVERT: A 504 LYS cc_start: 0.5971 (mptt) cc_final: 0.5544 (pptt) REVERT: A 548 THR cc_start: 0.5702 (t) cc_final: 0.5252 (t) REVERT: A 623 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.5987 (mm) REVERT: A 786 LEU cc_start: 0.7719 (tt) cc_final: 0.7365 (tt) REVERT: A 799 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6401 (tm-30) REVERT: A 889 LEU cc_start: 0.5417 (OUTLIER) cc_final: 0.5187 (mp) REVERT: A 947 LYS cc_start: 0.6559 (mmmt) cc_final: 0.6040 (mmtt) outliers start: 43 outliers final: 23 residues processed: 125 average time/residue: 0.0697 time to fit residues: 12.5209 Evaluate side-chains 116 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 832 GLN Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 970 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 ASN ** A 896 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 = 0.5128 r_free = 0.5128 target = 0.289445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5010 r_free = 0.5010 target = 0.249366 restraints weight = 10662.753| |-----------------------------------------------------------------------------| r_work (start): 0.4752 rms_B_bonded: 2.66 r_work: 0.4619 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 7306 Z= 0.194 Angle : 0.723 9.636 10114 Z= 0.376 Chirality : 0.049 0.254 1182 Planarity : 0.006 0.061 1110 Dihedral : 17.843 153.963 1524 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 6.88 % Allowed : 32.36 % 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: -2.32 (0.30), residues: 751 helix: -1.44 (0.35), residues: 204 sheet: -0.64 (0.44), residues: 152 loop : -1.96 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 366 TYR 0.026 0.002 TYR A 859 PHE 0.023 0.002 PHE A 970 TRP 0.016 0.002 TRP A 728 HIS 0.005 0.001 HIS A 893 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 7306) covalent geometry : angle 0.72302 / 0.38 (10114) hydrogen bonds : bond 0.05913 / 4.09 ( 256) hydrogen bonds : angle 5.76618 / 4.04 ( 663) *********************** 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 147 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 100 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 302 ILE cc_start: 0.5727 (OUTLIER) cc_final: 0.5477 (mp) REVERT: A 320 PHE cc_start: 0.4546 (OUTLIER) cc_final: 0.3689 (p90) REVERT: A 321 TYR cc_start: 0.6592 (m-10) cc_final: 0.5869 (m-10) REVERT: A 442 MET cc_start: 0.6380 (ptt) cc_final: 0.6164 (ptt) REVERT: A 450 PHE cc_start: 0.5756 (OUTLIER) cc_final: 0.5393 (t80) REVERT: A 504 LYS cc_start: 0.6291 (mptt) cc_final: 0.5827 (pptt) REVERT: A 526 HIS cc_start: 0.5030 (OUTLIER) cc_final: 0.4162 (m90) REVERT: A 548 THR cc_start: 0.5804 (t) cc_final: 0.5385 (t) REVERT: A 654 ILE cc_start: 0.6237 (OUTLIER) cc_final: 0.5985 (tp) REVERT: A 768 LYS cc_start: 0.5097 (OUTLIER) cc_final: 0.4790 (mmtt) REVERT: A 799 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6312 (tm-30) REVERT: A 889 LEU cc_start: 0.5650 (OUTLIER) cc_final: 0.5447 (mp) REVERT: A 947 LYS cc_start: 0.6644 (mmmt) cc_final: 0.6019 (mmtt) outliers start: 47 outliers final: 29 residues processed: 137 average time/residue: 0.0686 time to fit residues: 13.6450 Evaluate side-chains 127 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 785 SER Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 970 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 26 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 ASN A 718 GLN ** A 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5043 r_free = 0.5043 target = 0.256411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.222470 restraints weight = 9784.294| |-----------------------------------------------------------------------------| r_work (start): 0.4764 rms_B_bonded: 3.07 r_work: 0.4629 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7306 Z= 0.130 Angle : 0.675 9.837 10114 Z= 0.343 Chirality : 0.047 0.229 1182 Planarity : 0.006 0.061 1110 Dihedral : 17.902 154.060 1524 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 6.44 % Allowed : 32.65 % 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: -2.08 (0.30), residues: 751 helix: -1.25 (0.36), residues: 204 sheet: -0.51 (0.45), residues: 153 loop : -1.81 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 423 TYR 0.025 0.002 TYR A 944 PHE 0.019 0.002 PHE A 887 TRP 0.017 0.001 TRP A 728 HIS 0.006 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 7306) covalent geometry : angle 0.67454 / 0.34 (10114) hydrogen bonds : bond 0.05257 / 3.73 ( 256) hydrogen bonds : angle 5.66955 / 4.00 ( 663) *********************** 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 138 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 94 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 302 ILE cc_start: 0.5614 (OUTLIER) cc_final: 0.5269 (mp) REVERT: A 320 PHE cc_start: 0.4666 (OUTLIER) cc_final: 0.3932 (p90) REVERT: A 321 TYR cc_start: 0.6620 (m-10) cc_final: 0.5938 (m-10) REVERT: A 442 MET cc_start: 0.6400 (ptt) cc_final: 0.6098 (ptt) REVERT: A 450 PHE cc_start: 0.5922 (OUTLIER) cc_final: 0.5507 (t80) REVERT: A 504 LYS cc_start: 0.6205 (mptt) cc_final: 0.5727 (pptt) REVERT: A 526 HIS cc_start: 0.5038 (OUTLIER) cc_final: 0.4177 (m90) REVERT: A 548 THR cc_start: 0.5785 (t) cc_final: 0.5349 (t) REVERT: A 786 LEU cc_start: 0.8047 (tt) cc_final: 0.7734 (tt) REVERT: A 799 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6307 (tm-30) REVERT: A 889 LEU cc_start: 0.5530 (OUTLIER) cc_final: 0.5303 (mp) REVERT: A 927 HIS cc_start: 0.5808 (OUTLIER) cc_final: 0.5460 (m170) REVERT: A 947 LYS cc_start: 0.6680 (mmmt) cc_final: 0.6047 (mmtt) outliers start: 44 outliers final: 27 residues processed: 128 average time/residue: 0.0690 time to fit residues: 12.8401 Evaluate side-chains 127 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 970 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 9 optimal weight: 0.0070 chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 896 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 = 0.5111 r_free = 0.5111 target = 0.289228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5010 r_free = 0.5010 target = 0.247583 restraints weight = 10285.419| |-----------------------------------------------------------------------------| r_work (start): 0.4737 rms_B_bonded: 2.52 r_work: 0.4606 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7306 Z= 0.228 Angle : 0.750 9.770 10114 Z= 0.388 Chirality : 0.050 0.260 1182 Planarity : 0.006 0.062 1110 Dihedral : 17.849 153.258 1524 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 7.03 % Allowed : 33.24 % Favored : 59.74 % 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: -2.39 (0.30), residues: 751 helix: -1.40 (0.35), residues: 204 sheet: -0.81 (0.43), residues: 153 loop : -2.01 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 709 TYR 0.029 0.003 TYR A 944 PHE 0.023 0.002 PHE A 970 TRP 0.015 0.002 TRP A 728 HIS 0.005 0.001 HIS A 893 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.23 ( 7306) covalent geometry : angle 0.75024 / 0.39 (10114) hydrogen bonds : bond 0.05868 / 4.09 ( 256) hydrogen bonds : angle 5.85061 / 4.09 ( 663) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 92 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 302 ILE cc_start: 0.5720 (OUTLIER) cc_final: 0.5400 (mp) REVERT: A 320 PHE cc_start: 0.4962 (OUTLIER) cc_final: 0.4531 (p90) REVERT: A 321 TYR cc_start: 0.6661 (m-10) cc_final: 0.5996 (m-10) REVERT: A 442 MET cc_start: 0.6484 (ptt) cc_final: 0.6223 (ptt) REVERT: A 450 PHE cc_start: 0.6035 (OUTLIER) cc_final: 0.5577 (t80) REVERT: A 504 LYS cc_start: 0.6419 (mptt) cc_final: 0.5951 (tmmt) REVERT: A 526 HIS cc_start: 0.4958 (OUTLIER) cc_final: 0.4070 (m90) REVERT: A 548 THR cc_start: 0.5729 (t) cc_final: 0.5266 (t) REVERT: A 799 GLU cc_start: 0.6731 (mt-10) cc_final: 0.6332 (tm-30) REVERT: A 947 LYS cc_start: 0.6679 (mmmt) cc_final: 0.6086 (mmtt) outliers start: 48 outliers final: 36 residues processed: 129 average time/residue: 0.0657 time to fit residues: 12.3904 Evaluate side-chains 131 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 91 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 420 TYR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 785 SER Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 970 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 896 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 = 0.5131 r_free = 0.5131 target = 0.290117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.250259 restraints weight = 10577.369| |-----------------------------------------------------------------------------| r_work (start): 0.4755 rms_B_bonded: 2.63 r_work: 0.4629 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7306 Z= 0.150 Angle : 0.682 9.819 10114 Z= 0.352 Chirality : 0.048 0.240 1182 Planarity : 0.006 0.060 1110 Dihedral : 17.906 153.215 1524 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 6.44 % Allowed : 33.97 % Favored : 59.59 % 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: -2.27 (0.30), residues: 751 helix: -1.34 (0.35), residues: 204 sheet: -0.68 (0.45), residues: 155 loop : -1.95 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 423 TYR 0.028 0.002 TYR A 944 PHE 0.019 0.002 PHE A 970 TRP 0.017 0.002 TRP A 728 HIS 0.007 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 7306) covalent geometry : angle 0.68196 / 0.35 (10114) hydrogen bonds : bond 0.05378 / 3.81 ( 256) hydrogen bonds : angle 5.77619 / 4.05 ( 663) *********************** 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 138 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 94 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 302 ILE cc_start: 0.5632 (OUTLIER) cc_final: 0.5330 (mp) REVERT: A 320 PHE cc_start: 0.4829 (OUTLIER) cc_final: 0.4397 (p90) REVERT: A 321 TYR cc_start: 0.6657 (m-10) cc_final: 0.5958 (m-10) REVERT: A 442 MET cc_start: 0.6445 (ptt) cc_final: 0.6173 (ptt) REVERT: A 450 PHE cc_start: 0.6032 (OUTLIER) cc_final: 0.5606 (t80) REVERT: A 504 LYS cc_start: 0.6254 (mptt) cc_final: 0.5790 (tmmt) REVERT: A 526 HIS cc_start: 0.4942 (OUTLIER) cc_final: 0.4045 (m90) REVERT: A 548 THR cc_start: 0.5692 (t) cc_final: 0.5226 (t) REVERT: A 799 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6325 (tm-30) REVERT: A 927 HIS cc_start: 0.5784 (OUTLIER) cc_final: 0.5392 (m170) REVERT: A 947 LYS cc_start: 0.6612 (mmmt) cc_final: 0.6017 (mmtt) outliers start: 44 outliers final: 31 residues processed: 126 average time/residue: 0.0652 time to fit residues: 11.9325 Evaluate side-chains 128 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 970 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.287228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4987 r_free = 0.4987 target = 0.246501 restraints weight = 10629.514| |-----------------------------------------------------------------------------| r_work (start): 0.4722 rms_B_bonded: 2.62 r_work: 0.4592 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7306 Z= 0.215 Angle : 0.739 9.869 10114 Z= 0.382 Chirality : 0.050 0.260 1182 Planarity : 0.006 0.061 1110 Dihedral : 17.887 152.654 1524 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 6.00 % Allowed : 33.97 % Favored : 60.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.30), residues: 751 helix: -1.37 (0.35), residues: 204 sheet: -0.90 (0.44), residues: 153 loop : -2.05 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 709 TYR 0.027 0.003 TYR A 859 PHE 0.024 0.002 PHE A 970 TRP 0.016 0.002 TRP A 728 HIS 0.005 0.001 HIS A 893 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.22 ( 7306) covalent geometry : angle 0.73890 / 0.38 (10114) hydrogen bonds : bond 0.05821 / 4.08 ( 256) hydrogen bonds : angle 5.93450 / 4.14 ( 663) *********************** 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 133 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 302 ILE cc_start: 0.5707 (OUTLIER) cc_final: 0.5366 (mp) REVERT: A 320 PHE cc_start: 0.4554 (OUTLIER) cc_final: 0.4300 (p90) REVERT: A 321 TYR cc_start: 0.6775 (m-10) cc_final: 0.6068 (m-10) REVERT: A 442 MET cc_start: 0.6497 (ptt) cc_final: 0.6244 (ptt) REVERT: A 450 PHE cc_start: 0.6206 (OUTLIER) cc_final: 0.5725 (t80) REVERT: A 504 LYS cc_start: 0.6503 (mptt) cc_final: 0.6006 (tmmt) REVERT: A 526 HIS cc_start: 0.5017 (OUTLIER) cc_final: 0.4173 (m90) REVERT: A 548 THR cc_start: 0.5800 (t) cc_final: 0.5342 (t) REVERT: A 799 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6334 (tm-30) REVERT: A 927 HIS cc_start: 0.5985 (OUTLIER) cc_final: 0.5557 (m170) REVERT: A 947 LYS cc_start: 0.6671 (mmmt) cc_final: 0.6076 (mmtt) outliers start: 41 outliers final: 31 residues processed: 125 average time/residue: 0.0690 time to fit residues: 12.7041 Evaluate side-chains 131 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 785 SER Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 970 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.0020 chunk 68 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 ASN ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 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 = 0.5139 r_free = 0.5139 target = 0.292881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.5106 r_free = 0.5106 target = 0.254147 restraints weight = 10275.459| |-----------------------------------------------------------------------------| r_work (start): 0.4794 rms_B_bonded: 2.50 r_work: 0.4641 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7306 Z= 0.146 Angle : 0.685 10.103 10114 Z= 0.354 Chirality : 0.048 0.231 1182 Planarity : 0.006 0.060 1110 Dihedral : 17.896 152.714 1522 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 6.15 % Allowed : 34.11 % Favored : 59.74 % 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: -2.27 (0.30), residues: 751 helix: -1.29 (0.35), residues: 204 sheet: -0.76 (0.44), residues: 155 loop : -1.94 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 772 TYR 0.025 0.002 TYR A 944 PHE 0.020 0.002 PHE A 403 TRP 0.019 0.002 TRP A 728 HIS 0.007 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 7306) covalent geometry : angle 0.68492 / 0.35 (10114) hydrogen bonds : bond 0.05301 / 3.77 ( 256) hydrogen bonds : angle 5.82231 / 4.08 ( 663) *********************** 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 137 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 95 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 302 ILE cc_start: 0.5656 (OUTLIER) cc_final: 0.5398 (mp) REVERT: A 320 PHE cc_start: 0.4765 (OUTLIER) cc_final: 0.4390 (p90) REVERT: A 321 TYR cc_start: 0.6640 (m-10) cc_final: 0.5947 (m-10) REVERT: A 442 MET cc_start: 0.6579 (ptt) cc_final: 0.6271 (ptt) REVERT: A 450 PHE cc_start: 0.6176 (OUTLIER) cc_final: 0.5706 (t80) REVERT: A 504 LYS cc_start: 0.6129 (mptt) cc_final: 0.5814 (tmmt) REVERT: A 526 HIS cc_start: 0.4929 (OUTLIER) cc_final: 0.4035 (m90) REVERT: A 548 THR cc_start: 0.5772 (t) cc_final: 0.5313 (t) REVERT: A 665 GLN cc_start: 0.6643 (OUTLIER) cc_final: 0.6327 (pp30) REVERT: A 799 GLU cc_start: 0.6732 (mt-10) cc_final: 0.6323 (tm-30) REVERT: A 927 HIS cc_start: 0.5802 (OUTLIER) cc_final: 0.5410 (m170) REVERT: A 947 LYS cc_start: 0.6677 (mmmt) cc_final: 0.6047 (mmtt) outliers start: 42 outliers final: 30 residues processed: 128 average time/residue: 0.0687 time to fit residues: 12.8133 Evaluate side-chains 127 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 665 GLN Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 970 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 ASN ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5137 r_free = 0.5137 target = 0.292520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.251652 restraints weight = 10192.150| |-----------------------------------------------------------------------------| r_work (start): 0.4766 rms_B_bonded: 2.51 r_work: 0.4637 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6218 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 7306 Z= 0.206 Angle : 1.013 59.200 10114 Z= 0.576 Chirality : 0.049 0.318 1182 Planarity : 0.006 0.060 1110 Dihedral : 17.914 152.712 1522 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 5.71 % Allowed : 34.55 % Favored : 59.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.25 (0.30), residues: 751 helix: -1.28 (0.35), residues: 204 sheet: -0.73 (0.44), residues: 155 loop : -1.93 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 772 TYR 0.022 0.002 TYR A 944 PHE 0.019 0.002 PHE A 970 TRP 0.019 0.002 TRP A 728 HIS 0.007 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 ( 7306) covalent geometry : angle 1.01326 / 0.58 (10114) hydrogen bonds : bond 0.05302 / 3.78 ( 256) hydrogen bonds : angle 5.82439 / 4.08 ( 663) ********************** 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 130 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 302 ILE cc_start: 0.5637 (OUTLIER) cc_final: 0.5384 (mp) REVERT: A 320 PHE cc_start: 0.4762 (OUTLIER) cc_final: 0.4391 (p90) REVERT: A 321 TYR cc_start: 0.6629 (m-10) cc_final: 0.5937 (m-10) REVERT: A 442 MET cc_start: 0.6557 (ptt) cc_final: 0.6260 (ptt) REVERT: A 450 PHE cc_start: 0.6153 (OUTLIER) cc_final: 0.5699 (t80) REVERT: A 504 LYS cc_start: 0.6135 (mptt) cc_final: 0.5814 (tmmt) REVERT: A 526 HIS cc_start: 0.4929 (OUTLIER) cc_final: 0.4027 (m90) REVERT: A 548 THR cc_start: 0.5754 (t) cc_final: 0.5300 (t) REVERT: A 665 GLN cc_start: 0.6644 (OUTLIER) cc_final: 0.6329 (pp30) REVERT: A 752 MET cc_start: 0.4002 (ppp) cc_final: 0.3690 (ppp) REVERT: A 799 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6314 (tm-30) REVERT: A 927 HIS cc_start: 0.5780 (OUTLIER) cc_final: 0.5392 (m170) REVERT: A 947 LYS cc_start: 0.6674 (mmmt) cc_final: 0.6043 (mmtt) outliers start: 39 outliers final: 29 residues processed: 122 average time/residue: 0.0681 time to fit residues: 12.0829 Evaluate side-chains 126 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 586 TRP Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 665 GLN Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 877 HIS Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 970 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 59 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5135 r_free = 0.5135 target = 0.292224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.251161 restraints weight = 10238.744| |-----------------------------------------------------------------------------| r_work (start): 0.4763 rms_B_bonded: 2.54 r_work: 0.4636 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6218 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 7306 Z= 0.206 Angle : 1.013 59.200 10114 Z= 0.576 Chirality : 0.049 0.318 1182 Planarity : 0.006 0.060 1110 Dihedral : 17.914 152.712 1522 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 5.12 % Allowed : 34.70 % Favored : 60.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.25 (0.30), residues: 751 helix: -1.28 (0.35), residues: 204 sheet: -0.73 (0.44), residues: 155 loop : -1.93 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 772 TYR 0.022 0.002 TYR A 944 PHE 0.019 0.002 PHE A 970 TRP 0.019 0.002 TRP A 728 HIS 0.007 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 ( 7306) covalent geometry : angle 1.01327 / 0.58 (10114) hydrogen bonds : bond 0.05302 / 3.78 ( 256) hydrogen bonds : angle 5.82439 / 4.08 ( 663) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1794.59 seconds wall clock time: 31 minutes 38.79 seconds (1898.79 seconds total)