Starting phenix.real_space_refine on Tue Aug 4 19:50:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij0_60611/08_2026/9ij0_60611.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij0_60611/08_2026/9ij0_60611.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/9ij0_60611/08_2026/9ij0_60611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij0_60611/08_2026/9ij0_60611.map" model { file = "/net/cci-nas-00/data/ceres_data/9ij0_60611/08_2026/9ij0_60611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij0_60611/08_2026/9ij0_60611.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= 0.004 sd= 0.167 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 27 5.49 5 Mg 2 5.21 5 S 45 5.16 5 C 4156 2.51 5 N 1161 2.21 5 O 1276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6667 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 6091 Classifications: {'peptide': 758} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 720} Chain: "B" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'RNA': 19} Modifications used: {'rna2p': 1, 'rna2p_pyr': 3, 'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 15} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 175 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.62, per 1000 atoms: 0.24 Number of scatterers: 6667 At special positions: 0 Unit cell: (72.829, 90.221, 111.961, 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 45 16.00 P 27 15.00 Mg 2 11.99 O 1276 8.00 N 1161 7.00 C 4156 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: 0.36 Conformation dependent library (CDL) restraints added in 264.2 milliseconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1434 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 34.3% alpha, 25.3% beta 3 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 251 through 262 removed outlier: 3.775A pdb=" N ARG A 255 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS A 262 " --> pdb=" O MET A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 267 removed outlier: 3.805A pdb=" N THR A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 332 Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 404 through 412 Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'A' and resid 502 through 508 Processing helix chain 'A' and resid 508 through 520 removed outlier: 3.816A pdb=" N ASP A 514 " --> pdb=" O ARG A 510 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 540 Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 586 through 591 removed outlier: 3.644A pdb=" N VAL A 590 " --> pdb=" O TRP A 586 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR A 591 " --> pdb=" O VAL A 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 586 through 591' Processing helix chain 'A' and resid 612 through 631 removed outlier: 3.594A pdb=" N GLU A 618 " --> pdb=" O ASP A 614 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A 619 " --> pdb=" O GLN A 615 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 626 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLY A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 646 through 662 removed outlier: 3.684A pdb=" N GLY A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 688 removed outlier: 4.047A pdb=" N TYR A 679 " --> pdb=" O ARG A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 724 Processing helix chain 'A' and resid 781 through 802 Processing helix chain 'A' and resid 819 through 826 Processing helix chain 'A' and resid 826 through 833 Processing helix chain 'A' and resid 834 through 838 removed outlier: 3.665A pdb=" N ALA A 837 " --> pdb=" O CYS A 834 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE A 838 " --> pdb=" O PHE A 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 834 through 838' Processing helix chain 'A' and resid 914 through 926 Processing helix chain 'A' and resid 939 through 955 Processing sheet with id=AA1, first strand: chain 'A' and resid 769 through 776 removed outlier: 3.713A pdb=" N GLN A 776 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER A 754 " --> pdb=" O GLN A 776 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N VAL A 739 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL A 744 " --> pdb=" O ASP A 813 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 908 " --> pdb=" O VAL A 847 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL A 849 " --> pdb=" O CYS A 906 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N CYS A 906 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N GLN A 851 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR A 904 " --> pdb=" O GLN A 851 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL A 885 " --> pdb=" O CYS A 906 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 220 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N SER A 223 " --> pdb=" O ALA A 861 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 337 removed outlier: 3.724A pdb=" N ILE A 357 " --> pdb=" O MET A 348 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET A 348 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 337 removed outlier: 4.644A pdb=" N LEU A 372 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 271 through 272 removed outlier: 6.542A pdb=" N VAL A 238 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE A 309 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLN A 240 " --> pdb=" O THR A 307 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 423 through 426 removed outlier: 4.791A pdb=" N ILE A 415 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 429 through 431 Processing sheet with id=AA7, first strand: chain 'A' and resid 439 through 442 removed outlier: 3.628A pdb=" N LYS A 446 " --> pdb=" O MET A 442 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 576 through 579 Processing sheet with id=AA9, first strand: chain 'A' and resid 638 through 642 removed outlier: 6.479A pdb=" N ALA A 605 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE A 670 " --> pdb=" O ALA A 605 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N PHE A 607 " --> pdb=" O ILE A 670 " (cutoff:3.500A) 285 hydrogen bonds defined for protein. 813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 6 hydrogen bonds 12 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1004 1.30 - 1.43: 1897 1.43 - 1.56: 3848 1.56 - 1.69: 49 1.69 - 1.82: 71 Bond restraints: 6869 Sorted by residual: bond pdb=" C2 OMC B 26 " pdb=" N3 OMC B 26 " ideal model delta sigma weight residual 1.350 1.491 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C4 OMC B 26 " pdb=" N4 OMC B 26 " ideal model delta sigma weight residual 1.332 1.471 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" N3 OMC B 26 " pdb=" C4 OMC B 26 " ideal model delta sigma weight residual 1.317 1.453 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C5 OMC B 26 " pdb=" C6 OMC B 26 " ideal model delta sigma weight residual 1.346 1.480 -0.134 2.00e-02 2.50e+03 4.49e+01 bond pdb=" N1 OMC B 26 " pdb=" C6 OMC B 26 " ideal model delta sigma weight residual 1.357 1.455 -0.098 2.00e-02 2.50e+03 2.41e+01 ... (remaining 6864 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.13: 9373 4.13 - 8.26: 47 8.26 - 12.39: 4 12.39 - 16.53: 0 16.53 - 20.66: 2 Bond angle restraints: 9426 Sorted by residual: angle pdb=" O3' U B 25 " pdb=" P OMC B 26 " pdb=" OP1 OMC B 26 " ideal model delta sigma weight residual 108.00 87.34 20.66 3.00e+00 1.11e-01 4.74e+01 angle pdb=" O3' U B 25 " pdb=" P OMC B 26 " pdb=" OP2 OMC B 26 " ideal model delta sigma weight residual 108.00 88.41 19.59 3.00e+00 1.11e-01 4.26e+01 angle pdb=" C SER A 749 " pdb=" N ARG A 750 " pdb=" CA ARG A 750 " ideal model delta sigma weight residual 121.54 130.08 -8.54 1.91e+00 2.74e-01 2.00e+01 angle pdb=" O4' A B 10 " pdb=" C1' A B 10 " pdb=" C2' A B 10 " ideal model delta sigma weight residual 107.60 103.64 3.96 9.00e-01 1.23e+00 1.93e+01 angle pdb=" O3' C B 5 " pdb=" C3' C B 5 " pdb=" C2' C B 5 " ideal model delta sigma weight residual 113.70 106.72 6.98 1.60e+00 3.91e-01 1.90e+01 ... (remaining 9421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.82: 3699 19.82 - 39.63: 354 39.63 - 59.45: 77 59.45 - 79.26: 29 79.26 - 99.08: 6 Dihedral angle restraints: 4165 sinusoidal: 1947 harmonic: 2218 Sorted by residual: dihedral pdb=" CA PRO A 474 " pdb=" C PRO A 474 " pdb=" N SER A 475 " pdb=" CA SER A 475 " ideal model delta harmonic sigma weight residual 180.00 146.43 33.57 0 5.00e+00 4.00e-02 4.51e+01 dihedral pdb=" C3' A B 10 " pdb=" C4' A B 10 " pdb=" O4' A B 10 " pdb=" C1' A B 10 " ideal model delta sinusoidal sigma weight residual 20.00 -14.20 34.20 1 8.00e+00 1.56e-02 2.59e+01 dihedral pdb=" CA ASN A 399 " pdb=" C ASN A 399 " pdb=" N LYS A 400 " pdb=" CA LYS A 400 " ideal model delta harmonic sigma weight residual 180.00 155.39 24.61 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 4162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 818 0.047 - 0.095: 171 0.095 - 0.142: 76 0.142 - 0.190: 14 0.190 - 0.237: 6 Chirality restraints: 1085 Sorted by residual: chirality pdb=" C3' A B 3 " pdb=" C4' A B 3 " pdb=" O3' A B 3 " pdb=" C2' A B 3 " both_signs ideal model delta sigma weight residual False -2.48 -2.71 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C3' A B 12 " pdb=" C4' A B 12 " pdb=" O3' A B 12 " pdb=" C2' A B 12 " both_signs ideal model delta sigma weight residual False -2.48 -2.71 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C3' C B 11 " pdb=" C4' C B 11 " pdb=" O3' C B 11 " pdb=" C2' C B 11 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1082 not shown) Planarity restraints: 1097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 862 " -0.044 5.00e-02 4.00e+02 6.74e-02 7.26e+00 pdb=" N PRO A 863 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 863 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 863 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 343 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO A 344 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 652 " -0.183 9.50e-02 1.11e+02 8.23e-02 4.78e+00 pdb=" NE ARG A 652 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 652 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 652 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 652 " -0.002 2.00e-02 2.50e+03 ... (remaining 1094 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 10 2.39 - 3.01: 3572 3.01 - 3.64: 9693 3.64 - 4.27: 14536 4.27 - 4.90: 24924 Nonbonded interactions: 52735 Sorted by model distance: nonbonded pdb=" OP1 A B 3 " pdb="MG MG A1001 " model vdw 1.758 2.170 nonbonded pdb=" OXT LEU A 971 " pdb="MG MG A1001 " model vdw 1.861 2.170 nonbonded pdb=" OD2 ASP A 743 " pdb="MG MG A1002 " model vdw 1.999 2.170 nonbonded pdb=" OH TYR A 745 " pdb=" OE1 GLN A 954 " model vdw 2.109 3.040 nonbonded pdb=" O LEU A 490 " pdb=" O3' OMC B 26 " model vdw 2.193 3.040 ... (remaining 52730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.580 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 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 : 0.006 0.141 6869 Z= 0.320 Angle : 0.859 20.657 9426 Z= 0.472 Chirality : 0.052 0.237 1085 Planarity : 0.006 0.082 1097 Dihedral : 17.119 99.079 2731 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.82 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.30), residues: 756 helix: 1.30 (0.35), residues: 239 sheet: -0.36 (0.35), residues: 204 loop : -2.28 (0.31), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 652 TYR 0.010 0.001 TYR A 859 PHE 0.014 0.002 PHE A 758 TRP 0.019 0.001 TRP A 358 HIS 0.005 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.32 ( 6869) covalent geometry : angle 0.85934 / 0.47 ( 9426) hydrogen bonds : bond 0.15826 / 11.43 ( 285) hydrogen bonds : angle 7.23593 / 5.06 ( 825) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 622 MET cc_start: 0.6748 (tpp) cc_final: 0.6546 (tpp) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.0812 time to fit residues: 15.6385 Evaluate side-chains 84 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN A 704 GLN A 746 HIS A 825 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.188462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.134512 restraints weight = 7821.863| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.03 r_work: 0.3269 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 6869 Z= 0.301 Angle : 0.782 8.745 9426 Z= 0.408 Chirality : 0.052 0.324 1085 Planarity : 0.006 0.063 1097 Dihedral : 14.699 96.388 1207 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.48 % Favored : 93.25 % Rotamer: Outliers : 3.78 % Allowed : 14.85 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.30), residues: 756 helix: 1.25 (0.33), residues: 244 sheet: -0.45 (0.35), residues: 203 loop : -2.19 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 700 TYR 0.031 0.002 TYR A 859 PHE 0.017 0.003 PHE A 758 TRP 0.026 0.003 TRP A 358 HIS 0.010 0.002 HIS A 893 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.30 ( 6869) covalent geometry : angle 0.78165 / 0.41 ( 9426) hydrogen bonds : bond 0.05890 / 4.30 ( 285) hydrogen bonds : angle 5.76953 / 4.08 ( 825) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 255 ARG cc_start: 0.7262 (mtm-85) cc_final: 0.7012 (ttm110) REVERT: A 361 TYR cc_start: 0.8660 (m-80) cc_final: 0.8432 (m-80) REVERT: A 462 VAL cc_start: 0.7173 (OUTLIER) cc_final: 0.6925 (t) REVERT: A 608 TYR cc_start: 0.7753 (p90) cc_final: 0.7126 (p90) REVERT: A 613 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.6443 (ptm) outliers start: 26 outliers final: 14 residues processed: 102 average time/residue: 0.0834 time to fit residues: 11.6189 Evaluate side-chains 90 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 959 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 55 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.195201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.142014 restraints weight = 7801.287| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.97 r_work: 0.3324 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6869 Z= 0.147 Angle : 0.627 9.936 9426 Z= 0.328 Chirality : 0.045 0.152 1085 Planarity : 0.005 0.057 1097 Dihedral : 14.637 93.553 1207 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.82 % Favored : 93.92 % Rotamer: Outliers : 2.18 % Allowed : 17.03 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.30), residues: 756 helix: 1.69 (0.34), residues: 243 sheet: -0.25 (0.35), residues: 202 loop : -2.04 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 384 TYR 0.013 0.001 TYR A 859 PHE 0.016 0.002 PHE A 758 TRP 0.018 0.001 TRP A 358 HIS 0.003 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 6869) covalent geometry : angle 0.62689 / 0.33 ( 9426) hydrogen bonds : bond 0.04562 / 3.28 ( 285) hydrogen bonds : angle 5.44400 / 3.82 ( 825) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.242 Fit side-chains REVERT: A 361 TYR cc_start: 0.8610 (m-80) cc_final: 0.8340 (m-80) REVERT: A 386 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6604 (p0) REVERT: A 462 VAL cc_start: 0.7120 (OUTLIER) cc_final: 0.6911 (t) REVERT: A 498 MET cc_start: 0.7899 (mtp) cc_final: 0.7486 (mpp) REVERT: A 608 TYR cc_start: 0.7799 (p90) cc_final: 0.7171 (p90) REVERT: A 613 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6509 (ptm) outliers start: 15 outliers final: 5 residues processed: 91 average time/residue: 0.0863 time to fit residues: 10.7276 Evaluate side-chains 83 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 823 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 47 optimal weight: 0.0070 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 overall best weight: 2.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.187443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.131351 restraints weight = 7845.049| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.99 r_work: 0.3254 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6869 Z= 0.206 Angle : 0.626 8.093 9426 Z= 0.328 Chirality : 0.045 0.142 1085 Planarity : 0.005 0.055 1097 Dihedral : 14.588 92.041 1207 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.08 % Favored : 93.65 % Rotamer: Outliers : 2.91 % Allowed : 17.76 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.30), residues: 756 helix: 1.70 (0.34), residues: 243 sheet: -0.25 (0.36), residues: 203 loop : -2.04 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 255 TYR 0.016 0.001 TYR A 859 PHE 0.014 0.002 PHE A 758 TRP 0.021 0.002 TRP A 358 HIS 0.004 0.001 HIS A 893 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 ( 6869) covalent geometry : angle 0.62602 / 0.33 ( 9426) hydrogen bonds : bond 0.04658 / 3.36 ( 285) hydrogen bonds : angle 5.37198 / 3.78 ( 825) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.246 Fit side-chains REVERT: A 386 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.6248 (p0) REVERT: A 498 MET cc_start: 0.8177 (mtp) cc_final: 0.7343 (mpp) REVERT: A 608 TYR cc_start: 0.7425 (p90) cc_final: 0.7136 (p90) REVERT: A 613 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6542 (ptm) outliers start: 20 outliers final: 12 residues processed: 92 average time/residue: 0.0849 time to fit residues: 10.6632 Evaluate side-chains 88 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 873 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.9990 chunk 41 optimal weight: 0.0570 chunk 43 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 30.0000 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 GLN A 540 ASN A 819 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.187953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.131848 restraints weight = 7831.791| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.96 r_work: 0.3243 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6869 Z= 0.172 Angle : 0.599 10.032 9426 Z= 0.315 Chirality : 0.045 0.177 1085 Planarity : 0.004 0.053 1097 Dihedral : 14.603 90.284 1207 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.95 % Favored : 93.78 % Rotamer: Outliers : 2.47 % Allowed : 19.07 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.33 (0.31), residues: 756 helix: 1.82 (0.34), residues: 243 sheet: -0.15 (0.37), residues: 200 loop : -1.98 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 611 TYR 0.013 0.001 TYR A 859 PHE 0.016 0.002 PHE A 603 TRP 0.020 0.002 TRP A 358 HIS 0.003 0.001 HIS A 893 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 ( 6869) covalent geometry : angle 0.59949 / 0.31 ( 9426) hydrogen bonds : bond 0.04354 / 3.15 ( 285) hydrogen bonds : angle 5.30379 / 3.73 ( 825) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.250 Fit side-chains REVERT: A 498 MET cc_start: 0.8155 (mtp) cc_final: 0.7422 (mpp) REVERT: A 608 TYR cc_start: 0.7460 (p90) cc_final: 0.7199 (p90) REVERT: A 613 MET cc_start: 0.6795 (OUTLIER) cc_final: 0.6559 (ptm) REVERT: A 672 MET cc_start: 0.7239 (tpt) cc_final: 0.6895 (tpp) REVERT: A 782 ILE cc_start: 0.6210 (OUTLIER) cc_final: 0.5949 (mm) outliers start: 17 outliers final: 8 residues processed: 85 average time/residue: 0.0842 time to fit residues: 9.6661 Evaluate side-chains 81 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 873 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 GLN A 819 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.189433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.133073 restraints weight = 7875.775| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.08 r_work: 0.3250 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6869 Z= 0.150 Angle : 0.566 7.795 9426 Z= 0.300 Chirality : 0.044 0.149 1085 Planarity : 0.004 0.052 1097 Dihedral : 14.572 88.829 1207 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.82 % Favored : 93.92 % Rotamer: Outliers : 3.06 % Allowed : 19.07 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.31), residues: 756 helix: 1.87 (0.34), residues: 243 sheet: -0.02 (0.37), residues: 200 loop : -1.90 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 384 TYR 0.014 0.001 TYR A 679 PHE 0.016 0.002 PHE A 758 TRP 0.018 0.001 TRP A 358 HIS 0.006 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 6869) covalent geometry : angle 0.56615 / 0.30 ( 9426) hydrogen bonds : bond 0.04068 / 2.94 ( 285) hydrogen bonds : angle 5.22042 / 3.66 ( 825) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.249 Fit side-chains REVERT: A 498 MET cc_start: 0.8268 (mtp) cc_final: 0.7448 (mpp) REVERT: A 608 TYR cc_start: 0.7551 (p90) cc_final: 0.7249 (p90) REVERT: A 613 MET cc_start: 0.6698 (ttt) cc_final: 0.6432 (ptm) REVERT: A 672 MET cc_start: 0.7214 (tpt) cc_final: 0.6862 (tpp) REVERT: A 782 ILE cc_start: 0.6170 (OUTLIER) cc_final: 0.5897 (mm) REVERT: A 895 ARG cc_start: 0.8052 (ptp-110) cc_final: 0.7578 (ttm110) outliers start: 21 outliers final: 12 residues processed: 88 average time/residue: 0.0778 time to fit residues: 9.4564 Evaluate side-chains 86 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 873 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 57 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 GLN A 819 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.190801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134595 restraints weight = 7738.025| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 3.09 r_work: 0.3260 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6869 Z= 0.122 Angle : 0.568 11.049 9426 Z= 0.299 Chirality : 0.043 0.235 1085 Planarity : 0.004 0.051 1097 Dihedral : 14.551 87.895 1207 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.56 % Favored : 94.18 % Rotamer: Outliers : 2.33 % Allowed : 19.36 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.31), residues: 756 helix: 1.93 (0.34), residues: 244 sheet: 0.07 (0.38), residues: 200 loop : -1.92 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 354 TYR 0.009 0.001 TYR A 770 PHE 0.016 0.001 PHE A 758 TRP 0.015 0.001 TRP A 358 HIS 0.006 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 6869) covalent geometry : angle 0.56838 / 0.30 ( 9426) hydrogen bonds : bond 0.03723 / 2.69 ( 285) hydrogen bonds : angle 5.09354 / 3.57 ( 825) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.268 Fit side-chains REVERT: A 493 PRO cc_start: 0.8135 (Cg_exo) cc_final: 0.7892 (Cg_endo) REVERT: A 498 MET cc_start: 0.8133 (mtp) cc_final: 0.7377 (mpp) REVERT: A 608 TYR cc_start: 0.7545 (p90) cc_final: 0.7254 (p90) REVERT: A 613 MET cc_start: 0.6580 (ttt) cc_final: 0.6339 (ptm) REVERT: A 672 MET cc_start: 0.7189 (tpt) cc_final: 0.6884 (tpp) REVERT: A 895 ARG cc_start: 0.8041 (ptp-110) cc_final: 0.7511 (ttm110) outliers start: 16 outliers final: 12 residues processed: 89 average time/residue: 0.0848 time to fit residues: 10.2119 Evaluate side-chains 86 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 868 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 18 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 15 optimal weight: 0.2980 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS A 352 GLN A 380 HIS A 540 ASN A 819 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.185646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.129350 restraints weight = 7892.008| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.13 r_work: 0.3197 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 6869 Z= 0.289 Angle : 0.700 12.249 9426 Z= 0.360 Chirality : 0.048 0.156 1085 Planarity : 0.005 0.049 1097 Dihedral : 14.563 87.574 1207 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.95 % Favored : 93.78 % Rotamer: Outliers : 2.77 % Allowed : 19.51 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.31), residues: 756 helix: 1.68 (0.34), residues: 243 sheet: -0.28 (0.37), residues: 203 loop : -2.00 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 536 TYR 0.024 0.002 TYR A 679 PHE 0.017 0.003 PHE A 320 TRP 0.023 0.002 TRP A 358 HIS 0.014 0.002 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00709 / 0.29 ( 6869) covalent geometry : angle 0.70002 / 0.36 ( 9426) hydrogen bonds : bond 0.05015 / 3.62 ( 285) hydrogen bonds : angle 5.32090 / 3.76 ( 825) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.239 Fit side-chains REVERT: A 384 ARG cc_start: 0.6716 (mtt90) cc_final: 0.6219 (mtt90) REVERT: A 498 MET cc_start: 0.8205 (mtp) cc_final: 0.7527 (mpp) REVERT: A 608 TYR cc_start: 0.7696 (p90) cc_final: 0.7390 (p90) REVERT: A 613 MET cc_start: 0.7069 (ttt) cc_final: 0.6762 (ptm) REVERT: A 672 MET cc_start: 0.7315 (tpt) cc_final: 0.6931 (tpp) REVERT: A 864 ASP cc_start: 0.6252 (p0) cc_final: 0.5638 (p0) REVERT: A 882 CYS cc_start: 0.8503 (t) cc_final: 0.8125 (m) REVERT: A 895 ARG cc_start: 0.8079 (ptp-110) cc_final: 0.7592 (ttm110) outliers start: 19 outliers final: 9 residues processed: 93 average time/residue: 0.0845 time to fit residues: 10.5404 Evaluate side-chains 83 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 873 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 28 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 0.1980 chunk 19 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 GLN A 540 ASN A 819 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.189828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.123513 restraints weight = 7822.365| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.81 r_work: 0.3314 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 6869 Z= 0.129 Angle : 0.592 12.858 9426 Z= 0.309 Chirality : 0.043 0.138 1085 Planarity : 0.004 0.049 1097 Dihedral : 14.573 86.659 1207 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.03 % Favored : 94.71 % Rotamer: Outliers : 1.89 % Allowed : 20.82 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.31), residues: 756 helix: 1.91 (0.34), residues: 244 sheet: 0.04 (0.38), residues: 200 loop : -1.86 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 354 TYR 0.026 0.001 TYR A 679 PHE 0.016 0.002 PHE A 758 TRP 0.017 0.001 TRP A 358 HIS 0.014 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 6869) covalent geometry : angle 0.59194 / 0.31 ( 9426) hydrogen bonds : bond 0.03970 / 2.89 ( 285) hydrogen bonds : angle 5.12016 / 3.58 ( 825) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.234 Fit side-chains REVERT: A 498 MET cc_start: 0.8089 (mtp) cc_final: 0.7536 (mpp) REVERT: A 608 TYR cc_start: 0.7572 (p90) cc_final: 0.7222 (p90) REVERT: A 613 MET cc_start: 0.6935 (ttt) cc_final: 0.6661 (ptm) REVERT: A 672 MET cc_start: 0.7212 (tpt) cc_final: 0.6908 (tpp) REVERT: A 882 CYS cc_start: 0.8500 (t) cc_final: 0.8183 (m) REVERT: A 895 ARG cc_start: 0.8065 (ptp-110) cc_final: 0.7539 (ttm110) REVERT: A 928 MET cc_start: 0.8801 (mtp) cc_final: 0.8543 (mtp) outliers start: 13 outliers final: 11 residues processed: 85 average time/residue: 0.0871 time to fit residues: 9.9557 Evaluate side-chains 86 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 868 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 0.0030 chunk 48 optimal weight: 0.0670 overall best weight: 1.3532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 GLN A 819 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.189834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123538 restraints weight = 7812.083| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.79 r_work: 0.3296 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 6869 Z= 0.143 Angle : 0.611 12.987 9426 Z= 0.310 Chirality : 0.044 0.198 1085 Planarity : 0.004 0.048 1097 Dihedral : 14.512 86.033 1207 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.56 % Favored : 94.18 % Rotamer: Outliers : 1.60 % Allowed : 21.69 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.31), residues: 756 helix: 1.93 (0.34), residues: 243 sheet: 0.06 (0.38), residues: 200 loop : -1.84 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 354 TYR 0.021 0.001 TYR A 679 PHE 0.016 0.002 PHE A 758 TRP 0.017 0.001 TRP A 358 HIS 0.013 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 6869) covalent geometry : angle 0.61077 / 0.31 ( 9426) hydrogen bonds : bond 0.03874 / 2.80 ( 285) hydrogen bonds : angle 5.06982 / 3.56 ( 825) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.176 Fit side-chains REVERT: A 384 ARG cc_start: 0.6649 (mtt90) cc_final: 0.6127 (mtt90) REVERT: A 498 MET cc_start: 0.8075 (mtp) cc_final: 0.7498 (mpp) REVERT: A 608 TYR cc_start: 0.7596 (p90) cc_final: 0.7240 (p90) REVERT: A 613 MET cc_start: 0.6875 (ttt) cc_final: 0.6604 (ptm) REVERT: A 672 MET cc_start: 0.7209 (tpt) cc_final: 0.6897 (tpp) REVERT: A 882 CYS cc_start: 0.8503 (t) cc_final: 0.8157 (m) REVERT: A 895 ARG cc_start: 0.8055 (ptp-110) cc_final: 0.7527 (ttm110) REVERT: A 928 MET cc_start: 0.8787 (mtp) cc_final: 0.8517 (mtp) outliers start: 11 outliers final: 8 residues processed: 85 average time/residue: 0.0820 time to fit residues: 9.1091 Evaluate side-chains 84 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 868 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 57 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 59 optimal weight: 0.0570 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 GLN A 819 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.186901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120284 restraints weight = 7768.796| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.78 r_work: 0.3259 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 6869 Z= 0.239 Angle : 0.684 12.473 9426 Z= 0.344 Chirality : 0.047 0.225 1085 Planarity : 0.005 0.047 1097 Dihedral : 14.520 85.766 1207 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.69 % Favored : 94.05 % Rotamer: Outliers : 1.31 % Allowed : 21.40 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.31), residues: 756 helix: 1.75 (0.34), residues: 244 sheet: -0.11 (0.38), residues: 200 loop : -1.96 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 354 TYR 0.016 0.002 TYR A 679 PHE 0.016 0.002 PHE A 320 TRP 0.021 0.002 TRP A 358 HIS 0.019 0.002 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.24 ( 6869) covalent geometry : angle 0.68377 / 0.34 ( 9426) hydrogen bonds : bond 0.04609 / 3.33 ( 285) hydrogen bonds : angle 5.19313 / 3.66 ( 825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1741.91 seconds wall clock time: 30 minutes 32.58 seconds (1832.58 seconds total)