Starting phenix.real_space_refine on Thu Jul 2 05:21:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij1_60612/07_2026/9ij1_60612.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij1_60612/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ij1_60612/07_2026/9ij1_60612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij1_60612/07_2026/9ij1_60612.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ij1_60612/07_2026/9ij1_60612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij1_60612/07_2026/9ij1_60612.map" } 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): 0.01s 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: 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: 1.74, 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: 0.60 Conformation dependent library (CDL) restraints added in 343.2 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: 0.97 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: 1.41 Time building geometry restraints manager: 0.80 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: 9853 2.78 - 5.55: 203 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=" 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 angle pdb=" O2 U C 7 " pdb=" C2 U C 7 " pdb=" N3 U C 7 " ideal model delta sigma weight residual 122.20 118.26 3.94 7.00e-01 2.04e+00 3.16e+01 angle pdb=" N1 U C 7 " pdb=" C2 U C 7 " pdb=" O2 U C 7 " ideal model delta sigma weight residual 122.80 126.66 -3.86 7.00e-01 2.04e+00 3.04e+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: 903 0.060 - 0.120: 224 0.120 - 0.180: 48 0.180 - 0.240: 4 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.160 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: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.810 ------------------------------------------------------------------------------- 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= 0.256 Angle : 1.083 13.884 10114 Z= 0.659 Chirality : 0.057 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 0.00472 / 0.26 ( 7306) covalent geometry : angle 1.08333 / 0.66 (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 : 0.298 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: 0.0738 time to fit residues: 10.8039 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 : 0.215 ------------------------------------------------------------------------------- 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 518 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5150 r_free = 0.5150 target = 0.292739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5033 r_free = 0.5033 target = 0.251798 restraints weight = 10682.720| |-----------------------------------------------------------------------------| r_work (start): 0.4778 rms_B_bonded: 2.67 r_work: 0.4645 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7306 Z= 0.213 Angle : 0.734 8.897 10114 Z= 0.391 Chirality : 0.049 0.212 1182 Planarity : 0.007 0.063 1110 Dihedral : 18.018 160.192 1524 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 6.30 % Allowed : 32.65 % Favored : 61.05 % 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: -2.58 (0.29), residues: 751 helix: -1.71 (0.34), residues: 204 sheet: -0.70 (0.43), residues: 151 loop : -2.14 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 652 TYR 0.023 0.003 TYR A 859 PHE 0.034 0.003 PHE A 887 TRP 0.019 0.002 TRP A 728 HIS 0.006 0.001 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 ( 7306) covalent geometry : angle 0.73420 / 0.39 (10114) hydrogen bonds : bond 0.06253 / 4.41 ( 256) hydrogen bonds : angle 5.90684 / 4.10 ( 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 137 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 94 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 302 ILE cc_start: 0.5631 (OUTLIER) cc_final: 0.5348 (mp) REVERT: A 321 TYR cc_start: 0.6445 (m-10) cc_final: 0.5729 (m-10) REVERT: A 504 LYS cc_start: 0.5928 (mptt) cc_final: 0.5563 (pptt) REVERT: A 548 THR cc_start: 0.5682 (t) cc_final: 0.5217 (t) REVERT: A 623 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6283 (mm) REVERT: A 799 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6412 (tm-30) REVERT: A 889 LEU cc_start: 0.5738 (OUTLIER) cc_final: 0.5501 (mp) REVERT: A 947 LYS cc_start: 0.6713 (mmmt) cc_final: 0.6126 (mmtt) outliers start: 43 outliers final: 24 residues processed: 127 average time/residue: 0.0688 time to fit residues: 12.3975 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 : 0.179 ------------------------------------------------------------------------------- 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: 6.9990 chunk 71 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 8 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 713 GLN ** A 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5187 r_free = 0.5187 target = 0.297068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5077 r_free = 0.5077 target = 0.257006 restraints weight = 10513.119| |-----------------------------------------------------------------------------| r_work (start): 0.4812 rms_B_bonded: 2.66 r_work: 0.4683 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7306 Z= 0.126 Angle : 0.646 9.351 10114 Z= 0.339 Chirality : 0.046 0.197 1182 Planarity : 0.006 0.062 1110 Dihedral : 18.018 158.418 1524 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 5.86 % Allowed : 32.36 % Favored : 61.79 % 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: -2.29 (0.29), residues: 751 helix: -1.40 (0.35), residues: 204 sheet: -0.49 (0.44), residues: 149 loop : -2.01 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 366 TYR 0.018 0.002 TYR A 944 PHE 0.021 0.002 PHE A 887 TRP 0.017 0.001 TRP A 728 HIS 0.005 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 7306) covalent geometry : angle 0.64610 / 0.34 (10114) hydrogen bonds : bond 0.05482 / 3.89 ( 256) hydrogen bonds : angle 5.70242 / 4.00 ( 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 130 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 90 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 ILE cc_start: 0.5549 (OUTLIER) cc_final: 0.5245 (mp) REVERT: A 320 PHE cc_start: 0.4441 (OUTLIER) cc_final: 0.3680 (p90) REVERT: A 321 TYR cc_start: 0.6311 (m-10) cc_final: 0.5560 (m-10) REVERT: A 504 LYS cc_start: 0.5993 (mptt) cc_final: 0.5568 (pptt) REVERT: A 548 THR cc_start: 0.5711 (t) cc_final: 0.5236 (t) REVERT: A 623 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6012 (mm) REVERT: A 786 LEU cc_start: 0.7740 (tt) cc_final: 0.7392 (tt) REVERT: A 799 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6407 (tm-30) REVERT: A 889 LEU cc_start: 0.5439 (OUTLIER) cc_final: 0.5205 (mp) REVERT: A 947 LYS cc_start: 0.6570 (mmmt) cc_final: 0.6047 (mmtt) outliers start: 40 outliers final: 23 residues processed: 122 average time/residue: 0.0687 time to fit residues: 12.0073 Evaluate side-chains 114 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 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 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: 3.9990 chunk 46 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 = 0.5116 r_free = 0.5116 target = 0.289364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.247475 restraints weight = 10377.528| |-----------------------------------------------------------------------------| r_work (start): 0.4737 rms_B_bonded: 2.56 r_work: 0.4604 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7306 Z= 0.228 Angle : 0.743 9.001 10114 Z= 0.394 Chirality : 0.050 0.302 1182 Planarity : 0.006 0.061 1110 Dihedral : 17.925 154.600 1524 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 7.47 % Allowed : 32.21 % Favored : 60.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.29), residues: 751 helix: -1.52 (0.34), residues: 204 sheet: -0.74 (0.44), residues: 152 loop : -2.03 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 326 TYR 0.031 0.003 TYR A 859 PHE 0.024 0.003 PHE A 970 TRP 0.015 0.002 TRP A 728 HIS 0.006 0.002 HIS A 893 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.23 ( 7306) covalent geometry : angle 0.74313 / 0.39 (10114) hydrogen bonds : bond 0.06098 / 4.20 ( 256) hydrogen bonds : angle 5.93891 / 4.17 ( 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 150 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 99 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 302 ILE cc_start: 0.5810 (OUTLIER) cc_final: 0.5553 (mp) REVERT: A 320 PHE cc_start: 0.4757 (OUTLIER) cc_final: 0.4071 (p90) REVERT: A 321 TYR cc_start: 0.6725 (m-10) cc_final: 0.5988 (m-10) REVERT: A 442 MET cc_start: 0.6533 (ptt) cc_final: 0.6308 (ptt) REVERT: A 450 PHE cc_start: 0.5844 (OUTLIER) cc_final: 0.5476 (t80) REVERT: A 504 LYS cc_start: 0.6450 (mptt) cc_final: 0.5963 (tmmt) REVERT: A 526 HIS cc_start: 0.5087 (OUTLIER) cc_final: 0.4263 (m90) REVERT: A 548 THR cc_start: 0.5707 (t) cc_final: 0.5259 (t) REVERT: A 654 ILE cc_start: 0.6026 (OUTLIER) cc_final: 0.5760 (tp) REVERT: A 799 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6302 (tm-30) REVERT: A 889 LEU cc_start: 0.5698 (OUTLIER) cc_final: 0.5494 (mp) REVERT: A 947 LYS cc_start: 0.6631 (mmmt) cc_final: 0.6027 (mmtt) outliers start: 51 outliers final: 31 residues processed: 140 average time/residue: 0.0577 time to fit residues: 11.7878 Evaluate side-chains 126 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 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 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 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 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: 10.0000 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 38 optimal weight: 0.0870 chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.5155 r_free = 0.5155 target = 0.294040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.253273 restraints weight = 10213.792| |-----------------------------------------------------------------------------| r_work (start): 0.4777 rms_B_bonded: 2.55 r_work: 0.4647 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7306 Z= 0.137 Angle : 0.677 10.142 10114 Z= 0.350 Chirality : 0.047 0.197 1182 Planarity : 0.006 0.060 1110 Dihedral : 18.026 155.545 1524 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 6.30 % Allowed : 32.94 % 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: -2.21 (0.30), residues: 751 helix: -1.33 (0.35), residues: 204 sheet: -0.59 (0.44), residues: 155 loop : -1.91 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 423 TYR 0.015 0.002 TYR A 859 PHE 0.019 0.002 PHE A 887 TRP 0.018 0.001 TRP A 728 HIS 0.007 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 7306) covalent geometry : angle 0.67746 / 0.35 (10114) hydrogen bonds : bond 0.05213 / 3.72 ( 256) hydrogen bonds : angle 5.76090 / 4.06 ( 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 136 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 93 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 ILE cc_start: 0.5584 (OUTLIER) cc_final: 0.5299 (mp) REVERT: A 320 PHE cc_start: 0.4845 (OUTLIER) cc_final: 0.4212 (p90) REVERT: A 321 TYR cc_start: 0.6552 (m-10) cc_final: 0.5891 (m-10) REVERT: A 392 MET cc_start: 0.6825 (tpt) cc_final: 0.6536 (tpt) REVERT: A 442 MET cc_start: 0.6439 (ptt) cc_final: 0.6183 (ptt) REVERT: A 450 PHE cc_start: 0.5982 (OUTLIER) cc_final: 0.5571 (t80) REVERT: A 504 LYS cc_start: 0.6228 (mptt) cc_final: 0.5753 (tmmt) REVERT: A 526 HIS cc_start: 0.4973 (OUTLIER) cc_final: 0.4119 (m90) REVERT: A 548 THR cc_start: 0.5799 (t) cc_final: 0.5364 (t) REVERT: A 654 ILE cc_start: 0.6427 (OUTLIER) cc_final: 0.6219 (tp) REVERT: A 799 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6295 (tm-30) REVERT: A 889 LEU cc_start: 0.5548 (OUTLIER) cc_final: 0.5326 (mp) REVERT: A 927 HIS cc_start: 0.5810 (OUTLIER) cc_final: 0.5456 (m170) REVERT: A 947 LYS cc_start: 0.6558 (mmmt) cc_final: 0.5976 (mmtt) outliers start: 43 outliers final: 29 residues processed: 125 average time/residue: 0.0615 time to fit residues: 11.4562 Evaluate side-chains 126 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 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 654 ILE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 660 VAL 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 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 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: 0.7980 chunk 36 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 58 optimal weight: 0.3980 chunk 75 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 overall best weight: 3.0386 ------------------------------------------------------------------------------- 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 = 0.5101 r_free = 0.5101 target = 0.288180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4995 r_free = 0.4995 target = 0.246016 restraints weight = 10337.994| |-----------------------------------------------------------------------------| r_work (start): 0.4722 rms_B_bonded: 2.57 r_work: 0.4592 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7306 Z= 0.210 Angle : 0.724 9.714 10114 Z= 0.382 Chirality : 0.049 0.203 1182 Planarity : 0.006 0.060 1110 Dihedral : 17.953 153.528 1524 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 7.17 % Allowed : 32.50 % Favored : 60.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.30), residues: 751 helix: -1.33 (0.35), residues: 202 sheet: -0.85 (0.44), residues: 153 loop : -2.08 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 326 TYR 0.028 0.003 TYR A 859 PHE 0.023 0.002 PHE A 970 TRP 0.017 0.002 TRP A 728 HIS 0.005 0.001 HIS A 893 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 ( 7306) covalent geometry : angle 0.72439 / 0.38 (10114) hydrogen bonds : bond 0.05762 / 4.03 ( 256) hydrogen bonds : angle 5.88370 / 4.11 ( 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 144 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 95 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 302 ILE cc_start: 0.5768 (OUTLIER) cc_final: 0.5451 (mp) REVERT: A 320 PHE cc_start: 0.4840 (OUTLIER) cc_final: 0.4594 (p90) REVERT: A 321 TYR cc_start: 0.6749 (m-10) cc_final: 0.6065 (m-10) REVERT: A 392 MET cc_start: 0.6820 (tpt) cc_final: 0.6529 (tpt) REVERT: A 442 MET cc_start: 0.6525 (ptt) cc_final: 0.6304 (ptt) REVERT: A 450 PHE cc_start: 0.6108 (OUTLIER) cc_final: 0.5654 (t80) REVERT: A 504 LYS cc_start: 0.6339 (mptt) cc_final: 0.5866 (tmmt) REVERT: A 526 HIS cc_start: 0.4957 (OUTLIER) cc_final: 0.4119 (m90) REVERT: A 548 THR cc_start: 0.5746 (t) cc_final: 0.5286 (t) REVERT: A 947 LYS cc_start: 0.6635 (mmmt) cc_final: 0.6060 (mmtt) outliers start: 49 outliers final: 34 residues processed: 133 average time/residue: 0.0576 time to fit residues: 11.1822 Evaluate side-chains 130 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 92 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 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 501 ILE 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 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: 2.9990 chunk 9 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 72 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.5001 r_free = 0.5001 target = 0.251422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.216388 restraints weight = 10102.722| |-----------------------------------------------------------------------------| r_work (start): 0.4704 rms_B_bonded: 3.11 r_work: 0.4568 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7306 Z= 0.171 Angle : 0.694 10.754 10114 Z= 0.362 Chirality : 0.048 0.200 1182 Planarity : 0.006 0.060 1110 Dihedral : 18.012 153.958 1524 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 6.15 % Allowed : 33.24 % Favored : 60.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.30), residues: 751 helix: -1.32 (0.35), residues: 204 sheet: -0.74 (0.45), residues: 155 loop : -1.99 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 423 TYR 0.023 0.002 TYR A 944 PHE 0.022 0.002 PHE A 970 TRP 0.017 0.002 TRP A 728 HIS 0.006 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 7306) covalent geometry : angle 0.69382 / 0.36 (10114) hydrogen bonds : bond 0.05376 / 3.81 ( 256) hydrogen bonds : angle 5.85791 / 4.10 ( 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 135 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 302 ILE cc_start: 0.5736 (OUTLIER) cc_final: 0.5431 (mp) REVERT: A 320 PHE cc_start: 0.4725 (OUTLIER) cc_final: 0.4400 (p90) REVERT: A 321 TYR cc_start: 0.6777 (m-10) cc_final: 0.6056 (m-10) REVERT: A 334 MET cc_start: 0.8061 (mtt) cc_final: 0.7858 (mtt) REVERT: A 392 MET cc_start: 0.6841 (tpt) cc_final: 0.6562 (tpt) REVERT: A 442 MET cc_start: 0.6567 (ptt) cc_final: 0.6298 (ptt) REVERT: A 450 PHE cc_start: 0.6203 (OUTLIER) cc_final: 0.5727 (t80) REVERT: A 504 LYS cc_start: 0.6342 (mptt) cc_final: 0.5867 (tmmt) REVERT: A 526 HIS cc_start: 0.5072 (OUTLIER) cc_final: 0.4237 (m90) REVERT: A 548 THR cc_start: 0.5760 (t) cc_final: 0.5301 (t) REVERT: A 799 GLU cc_start: 0.6698 (mt-10) cc_final: 0.6348 (tm-30) REVERT: A 927 HIS cc_start: 0.5963 (OUTLIER) cc_final: 0.5528 (m170) REVERT: A 947 LYS cc_start: 0.6581 (mmmt) cc_final: 0.6017 (mmtt) outliers start: 42 outliers final: 30 residues processed: 126 average time/residue: 0.0591 time to fit residues: 10.7748 Evaluate side-chains 125 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 38 optimal weight: 0.0370 chunk 42 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 56 optimal weight: 0.0370 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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 = 0.5141 r_free = 0.5141 target = 0.292768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5033 r_free = 0.5033 target = 0.252483 restraints weight = 10593.991| |-----------------------------------------------------------------------------| r_work (start): 0.4767 rms_B_bonded: 2.65 r_work: 0.4638 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7306 Z= 0.126 Angle : 0.659 10.502 10114 Z= 0.342 Chirality : 0.046 0.180 1182 Planarity : 0.006 0.059 1110 Dihedral : 18.036 154.423 1524 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 5.71 % Allowed : 33.67 % Favored : 60.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.30), residues: 751 helix: -1.15 (0.36), residues: 204 sheet: -0.62 (0.44), residues: 155 loop : -1.89 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 423 TYR 0.034 0.002 TYR A 944 PHE 0.019 0.002 PHE A 970 TRP 0.020 0.002 TRP A 728 HIS 0.007 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 7306) covalent geometry : angle 0.65855 / 0.34 (10114) hydrogen bonds : bond 0.05043 / 3.63 ( 256) hydrogen bonds : angle 5.67382 / 3.98 ( 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 137 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 98 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 ILE cc_start: 0.5631 (OUTLIER) cc_final: 0.5377 (mp) REVERT: A 320 PHE cc_start: 0.4658 (OUTLIER) cc_final: 0.4288 (p90) REVERT: A 321 TYR cc_start: 0.6664 (m-10) cc_final: 0.5973 (m-10) REVERT: A 392 MET cc_start: 0.6747 (tpt) cc_final: 0.6453 (tpt) REVERT: A 442 MET cc_start: 0.6535 (ptt) cc_final: 0.6264 (ptt) REVERT: A 450 PHE cc_start: 0.6076 (OUTLIER) cc_final: 0.5600 (t80) REVERT: A 504 LYS cc_start: 0.6092 (mptt) cc_final: 0.5796 (tmmt) REVERT: A 526 HIS cc_start: 0.5073 (OUTLIER) cc_final: 0.4188 (m90) REVERT: A 548 THR cc_start: 0.5721 (t) cc_final: 0.5257 (t) REVERT: A 661 GLU cc_start: 0.4474 (OUTLIER) cc_final: 0.3898 (pm20) REVERT: A 799 GLU cc_start: 0.6746 (mt-10) cc_final: 0.6327 (tm-30) REVERT: A 927 HIS cc_start: 0.5897 (OUTLIER) cc_final: 0.5524 (m170) REVERT: A 947 LYS cc_start: 0.6719 (mmmt) cc_final: 0.6115 (mmtt) outliers start: 39 outliers final: 30 residues processed: 128 average time/residue: 0.0618 time to fit residues: 11.4467 Evaluate side-chains 130 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE 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 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 661 GLU 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 832 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 38 optimal weight: 0.0670 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- 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 = 0.4989 r_free = 0.4989 target = 0.250098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.217844 restraints weight = 9860.784| |-----------------------------------------------------------------------------| r_work (start): 0.4722 rms_B_bonded: 3.13 r_work: 0.4571 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7306 Z= 0.199 Angle : 0.715 10.415 10114 Z= 0.372 Chirality : 0.048 0.187 1182 Planarity : 0.006 0.059 1110 Dihedral : 17.952 153.154 1524 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 6.00 % Allowed : 33.53 % Favored : 60.47 % 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: -2.26 (0.30), residues: 751 helix: -1.22 (0.36), residues: 204 sheet: -0.75 (0.44), residues: 155 loop : -1.98 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 709 TYR 0.028 0.002 TYR A 944 PHE 0.024 0.002 PHE A 970 TRP 0.017 0.001 TRP A 728 HIS 0.005 0.001 HIS A 893 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 ( 7306) covalent geometry : angle 0.71494 / 0.37 (10114) hydrogen bonds : bond 0.05527 / 3.90 ( 256) hydrogen bonds : angle 5.81811 / 4.06 ( 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 135 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 94 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 302 ILE cc_start: 0.5726 (OUTLIER) cc_final: 0.5416 (mp) REVERT: A 320 PHE cc_start: 0.4414 (OUTLIER) cc_final: 0.4195 (p90) REVERT: A 321 TYR cc_start: 0.6794 (m-10) cc_final: 0.6075 (m-10) REVERT: A 369 ASP cc_start: 0.7012 (m-30) cc_final: 0.6801 (m-30) REVERT: A 442 MET cc_start: 0.6636 (ptt) cc_final: 0.6347 (ptt) REVERT: A 450 PHE cc_start: 0.6165 (OUTLIER) cc_final: 0.5640 (t80) REVERT: A 504 LYS cc_start: 0.6210 (mptt) cc_final: 0.5894 (tmmt) REVERT: A 526 HIS cc_start: 0.5026 (OUTLIER) cc_final: 0.4195 (m90) REVERT: A 548 THR cc_start: 0.5716 (t) cc_final: 0.5273 (t) REVERT: A 661 GLU cc_start: 0.4616 (OUTLIER) cc_final: 0.4113 (pm20) REVERT: A 799 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6338 (tm-30) REVERT: A 927 HIS cc_start: 0.5987 (OUTLIER) cc_final: 0.5486 (m170) REVERT: A 947 LYS cc_start: 0.6616 (mmmt) cc_final: 0.6040 (mmtt) outliers start: 41 outliers final: 32 residues processed: 126 average time/residue: 0.0530 time to fit residues: 9.9997 Evaluate side-chains 130 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 92 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE 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 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 661 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 23 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 13 optimal weight: 0.3980 chunk 71 optimal weight: 3.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- 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 = 0.4965 r_free = 0.4965 target = 0.247415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.212796 restraints weight = 9802.385| |-----------------------------------------------------------------------------| r_work (start): 0.4674 rms_B_bonded: 3.04 r_work: 0.4542 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7306 Z= 0.237 Angle : 0.763 10.565 10114 Z= 0.398 Chirality : 0.050 0.200 1182 Planarity : 0.006 0.060 1110 Dihedral : 17.996 152.779 1524 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 6.00 % Allowed : 33.82 % Favored : 60.18 % 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: -2.44 (0.30), residues: 751 helix: -1.26 (0.36), residues: 200 sheet: -0.95 (0.44), residues: 155 loop : -2.11 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 423 TYR 0.030 0.003 TYR A 859 PHE 0.025 0.002 PHE A 970 TRP 0.014 0.002 TRP A 728 HIS 0.005 0.001 HIS A 893 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.24 ( 7306) covalent geometry : angle 0.76291 / 0.40 (10114) hydrogen bonds : bond 0.05853 / 4.11 ( 256) hydrogen bonds : angle 6.01239 / 4.18 ( 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 129 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 88 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 302 ILE cc_start: 0.5774 (OUTLIER) cc_final: 0.5462 (mp) REVERT: A 321 TYR cc_start: 0.6899 (m-10) cc_final: 0.6190 (m-10) REVERT: A 392 MET cc_start: 0.7026 (tpt) cc_final: 0.6764 (tpt) REVERT: A 442 MET cc_start: 0.6652 (ptt) cc_final: 0.6403 (ptt) REVERT: A 450 PHE cc_start: 0.6198 (OUTLIER) cc_final: 0.5671 (t80) REVERT: A 504 LYS cc_start: 0.6306 (mptt) cc_final: 0.5965 (tmmt) REVERT: A 526 HIS cc_start: 0.5018 (OUTLIER) cc_final: 0.4159 (m90) REVERT: A 548 THR cc_start: 0.5724 (t) cc_final: 0.5302 (t) REVERT: A 661 GLU cc_start: 0.4676 (OUTLIER) cc_final: 0.4134 (pm20) REVERT: A 927 HIS cc_start: 0.6096 (OUTLIER) cc_final: 0.5551 (m170) REVERT: A 947 LYS cc_start: 0.6592 (mmmt) cc_final: 0.6030 (mmtt) outliers start: 41 outliers final: 32 residues processed: 121 average time/residue: 0.0519 time to fit residues: 9.5946 Evaluate side-chains 128 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 328 VAL Chi-restraints excluded: chain A residue 379 SER 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 462 VAL 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 661 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 59 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** 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 = 0.4974 r_free = 0.4974 target = 0.248442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.216100 restraints weight = 9849.049| |-----------------------------------------------------------------------------| r_work (start): 0.4703 rms_B_bonded: 3.09 r_work: 0.4551 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.4551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7306 Z= 0.196 Angle : 0.747 10.612 10114 Z= 0.386 Chirality : 0.050 0.221 1182 Planarity : 0.006 0.060 1110 Dihedral : 17.989 153.133 1522 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 5.27 % Allowed : 34.26 % Favored : 60.47 % 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: -2.44 (0.30), residues: 751 helix: -1.17 (0.36), residues: 196 sheet: -0.92 (0.44), residues: 155 loop : -2.17 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 423 TYR 0.029 0.002 TYR A 944 PHE 0.024 0.002 PHE A 970 TRP 0.016 0.002 TRP A 728 HIS 0.007 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 ( 7306) covalent geometry : angle 0.74670 / 0.39 (10114) hydrogen bonds : bond 0.05605 / 3.96 ( 256) hydrogen bonds : angle 6.01530 / 4.19 ( 663) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1631.99 seconds wall clock time: 28 minutes 46.73 seconds (1726.73 seconds total)