Starting phenix.real_space_refine on Thu Jul 2 03:54:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij0_60611/07_2026/9ij0_60611.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij0_60611/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ij0_60611/07_2026/9ij0_60611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij0_60611/07_2026/9ij0_60611.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ij0_60611/07_2026/9ij0_60611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij0_60611/07_2026/9ij0_60611.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= 0.004 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-dev-6108/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: 0.57 Conformation dependent library (CDL) restraints added in 358.7 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: 0.76 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: 1.09 Time building geometry restraints manager: 0.77 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: 9375 4.13 - 8.26: 46 8.26 - 12.39: 3 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=" O2' A B 3 " pdb=" C2' A B 3 " pdb=" C1' A B 3 " ideal model delta sigma weight residual 108.40 98.59 9.81 1.50e+00 4.44e-01 4.28e+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=" 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 1.50e+00 4.44e-01 2.17e+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 ... (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: 825 0.047 - 0.095: 169 0.095 - 0.142: 70 0.142 - 0.190: 16 0.190 - 0.237: 5 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: 0.190 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: 0.030 Set scattering table: 0.020 Process input model: 7.970 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.500 ------------------------------------------------------------------------------- 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= 0.298 Angle : 0.846 20.657 9426 Z= 0.466 Chirality : 0.051 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 0.00579 / 0.30 ( 6869) covalent geometry : angle 0.84648 / 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 : 0.225 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: 0.1015 time to fit residues: 19.7599 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 : 0.242 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.188713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134354 restraints weight = 7821.945| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.12 r_work: 0.3256 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 6869 Z= 0.300 Angle : 0.771 8.609 9426 Z= 0.403 Chirality : 0.052 0.383 1085 Planarity : 0.006 0.063 1097 Dihedral : 14.817 95.765 1207 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.08 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: -0.86 (0.30), residues: 756 helix: 1.25 (0.34), residues: 244 sheet: -0.45 (0.35), residues: 203 loop : -2.20 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 700 TYR 0.032 0.002 TYR A 859 PHE 0.018 0.003 PHE A 758 TRP 0.025 0.003 TRP A 358 HIS 0.010 0.002 HIS A 893 Details of bonding type rmsd/Z covalent geometry : bond 0.00725 / 0.30 ( 6869) covalent geometry : angle 0.77062 / 0.40 ( 9426) hydrogen bonds : bond 0.05935 / 4.34 ( 285) hydrogen bonds : angle 5.78541 / 4.09 ( 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 113 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 361 TYR cc_start: 0.8657 (m-80) cc_final: 0.8445 (m-80) REVERT: A 462 VAL cc_start: 0.7073 (OUTLIER) cc_final: 0.6839 (t) REVERT: A 608 TYR cc_start: 0.7733 (p90) cc_final: 0.7116 (p90) REVERT: A 613 MET cc_start: 0.6812 (OUTLIER) cc_final: 0.6428 (ptm) REVERT: A 679 TYR cc_start: 0.7908 (t80) cc_final: 0.7260 (t80) outliers start: 26 outliers final: 14 residues processed: 104 average time/residue: 0.0723 time to fit residues: 10.2080 Evaluate side-chains 89 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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: 0.8980 chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 540 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.196447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.143151 restraints weight = 7777.005| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.02 r_work: 0.3398 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6869 Z= 0.135 Angle : 0.615 10.750 9426 Z= 0.322 Chirality : 0.045 0.199 1085 Planarity : 0.005 0.058 1097 Dihedral : 14.741 93.512 1207 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.16 % Favored : 94.58 % Rotamer: Outliers : 2.04 % Allowed : 17.18 % 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: -0.44 (0.30), residues: 756 helix: 1.70 (0.34), residues: 243 sheet: -0.22 (0.36), residues: 202 loop : -2.02 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 920 TYR 0.011 0.001 TYR A 425 PHE 0.018 0.002 PHE A 607 TRP 0.017 0.001 TRP A 358 HIS 0.003 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 6869) covalent geometry : angle 0.61470 / 0.32 ( 9426) hydrogen bonds : bond 0.04380 / 3.15 ( 285) hydrogen bonds : angle 5.41174 / 3.79 ( 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 98 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.216 Fit side-chains REVERT: A 361 TYR cc_start: 0.8592 (m-80) cc_final: 0.8330 (m-80) REVERT: A 386 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6647 (p0) REVERT: A 462 VAL cc_start: 0.7143 (OUTLIER) cc_final: 0.6933 (t) REVERT: A 498 MET cc_start: 0.7849 (mtp) cc_final: 0.7514 (mpp) REVERT: A 608 TYR cc_start: 0.7838 (p90) cc_final: 0.7238 (p90) REVERT: A 613 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6481 (ptm) REVERT: A 679 TYR cc_start: 0.7895 (t80) cc_final: 0.7346 (t80) outliers start: 14 outliers final: 5 residues processed: 92 average time/residue: 0.0770 time to fit residues: 9.6776 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 : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 VAL 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 823 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS A 352 GLN A 540 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.184244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128141 restraints weight = 7936.124| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.23 r_work: 0.3157 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 6869 Z= 0.330 Angle : 0.748 8.496 9426 Z= 0.389 Chirality : 0.049 0.200 1085 Planarity : 0.006 0.055 1097 Dihedral : 14.660 92.291 1207 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.95 % Favored : 93.78 % Rotamer: Outliers : 3.20 % Allowed : 18.20 % Favored : 78.60 % 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: -0.79 (0.30), residues: 756 helix: 1.37 (0.33), residues: 243 sheet: -0.44 (0.36), residues: 203 loop : -2.17 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 255 TYR 0.023 0.002 TYR A 859 PHE 0.017 0.003 PHE A 848 TRP 0.029 0.003 TRP A 358 HIS 0.007 0.002 HIS A 893 Details of bonding type rmsd/Z covalent geometry : bond 0.00807 / 0.33 ( 6869) covalent geometry : angle 0.74790 / 0.39 ( 9426) hydrogen bonds : bond 0.05631 / 4.05 ( 285) hydrogen bonds : angle 5.62092 / 3.96 ( 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 97 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.219 Fit side-chains REVERT: A 386 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.6238 (p0) REVERT: A 462 VAL cc_start: 0.6865 (OUTLIER) cc_final: 0.6664 (t) REVERT: A 498 MET cc_start: 0.8191 (mtp) cc_final: 0.7396 (mpp) REVERT: A 608 TYR cc_start: 0.7650 (p90) cc_final: 0.7396 (p90) REVERT: A 613 MET cc_start: 0.6928 (ttt) cc_final: 0.6659 (ptm) REVERT: A 617 ARG cc_start: 0.6432 (mmt180) cc_final: 0.6229 (mmt180) REVERT: A 645 ASP cc_start: 0.7483 (m-30) cc_final: 0.7277 (m-30) REVERT: A 679 TYR cc_start: 0.7590 (t80) cc_final: 0.7347 (t80) outliers start: 22 outliers final: 12 residues processed: 89 average time/residue: 0.0703 time to fit residues: 8.6031 Evaluate side-chains 87 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 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 767 THR 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: 3.9990 chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.0020 chunk 35 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.190162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.133634 restraints weight = 7829.623| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.24 r_work: 0.3238 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6869 Z= 0.124 Angle : 0.575 9.477 9426 Z= 0.306 Chirality : 0.044 0.191 1085 Planarity : 0.004 0.055 1097 Dihedral : 14.670 90.635 1207 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.03 % Favored : 94.71 % Rotamer: Outliers : 2.18 % Allowed : 19.21 % Favored : 78.60 % 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: -0.09 (0.37), residues: 200 loop : -1.97 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 920 TYR 0.011 0.001 TYR A 770 PHE 0.017 0.002 PHE A 607 TRP 0.017 0.001 TRP A 358 HIS 0.005 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 6869) covalent geometry : angle 0.57544 / 0.31 ( 9426) hydrogen bonds : bond 0.04032 / 2.92 ( 285) hydrogen bonds : angle 5.29680 / 3.71 ( 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: 15 poor density : 77 time to evaluate : 0.213 Fit side-chains REVERT: A 462 VAL cc_start: 0.6735 (OUTLIER) cc_final: 0.6528 (t) REVERT: A 498 MET cc_start: 0.8268 (mtp) cc_final: 0.7493 (mpp) REVERT: A 608 TYR cc_start: 0.7523 (p90) cc_final: 0.6824 (p90) REVERT: A 613 MET cc_start: 0.6815 (ttt) cc_final: 0.6401 (ptm) REVERT: A 679 TYR cc_start: 0.7526 (t80) cc_final: 0.6893 (t80) REVERT: A 782 ILE cc_start: 0.6192 (OUTLIER) cc_final: 0.5924 (mm) outliers start: 15 outliers final: 5 residues processed: 87 average time/residue: 0.0804 time to fit residues: 9.4248 Evaluate side-chains 80 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 MET 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 622 MET Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 823 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 64 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.189198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132385 restraints weight = 7874.265| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.04 r_work: 0.3240 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3697 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= 0.148 Angle : 0.572 7.150 9426 Z= 0.304 Chirality : 0.044 0.252 1085 Planarity : 0.004 0.052 1097 Dihedral : 14.577 89.709 1207 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.82 % Favored : 93.92 % Rotamer: Outliers : 2.33 % Allowed : 19.51 % Favored : 78.17 % 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: -0.25 (0.31), residues: 756 helix: 1.85 (0.34), residues: 243 sheet: -0.07 (0.37), residues: 200 loop : -1.92 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 611 TYR 0.011 0.001 TYR A 859 PHE 0.015 0.002 PHE A 607 TRP 0.018 0.001 TRP A 358 HIS 0.009 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 6869) covalent geometry : angle 0.57150 / 0.30 ( 9426) hydrogen bonds : bond 0.04032 / 2.92 ( 285) hydrogen bonds : angle 5.23016 / 3.67 ( 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 91 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.176 Fit side-chains REVERT: A 462 VAL cc_start: 0.6882 (OUTLIER) cc_final: 0.6511 (t) REVERT: A 493 PRO cc_start: 0.8199 (Cg_exo) cc_final: 0.7982 (Cg_endo) REVERT: A 498 MET cc_start: 0.8343 (mtp) cc_final: 0.7446 (mpp) REVERT: A 608 TYR cc_start: 0.7510 (p90) cc_final: 0.7191 (p90) REVERT: A 613 MET cc_start: 0.6687 (ttt) cc_final: 0.6469 (ptm) REVERT: A 679 TYR cc_start: 0.7480 (t80) cc_final: 0.6798 (t80) REVERT: A 782 ILE cc_start: 0.6134 (OUTLIER) cc_final: 0.5862 (mm) REVERT: A 895 ARG cc_start: 0.8067 (ptp-110) cc_final: 0.7587 (ttm110) outliers start: 16 outliers final: 8 residues processed: 86 average time/residue: 0.0595 time to fit residues: 6.8940 Evaluate side-chains 83 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 430 VAL Chi-restraints excluded: chain A residue 462 VAL 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 868 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 57 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 41 optimal weight: 0.0870 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.190964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124825 restraints weight = 7727.356| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.80 r_work: 0.3308 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6869 Z= 0.115 Angle : 0.576 10.569 9426 Z= 0.299 Chirality : 0.043 0.188 1085 Planarity : 0.004 0.050 1097 Dihedral : 14.557 88.849 1207 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.56 % Favored : 94.18 % Rotamer: Outliers : 2.04 % Allowed : 20.82 % Favored : 77.15 % 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: -0.13 (0.31), residues: 756 helix: 1.92 (0.34), residues: 244 sheet: 0.02 (0.37), residues: 200 loop : -1.86 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 920 TYR 0.009 0.001 TYR A 770 PHE 0.016 0.002 PHE A 758 TRP 0.014 0.001 TRP A 358 HIS 0.010 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 6869) covalent geometry : angle 0.57563 / 0.30 ( 9426) hydrogen bonds : bond 0.03673 / 2.66 ( 285) hydrogen bonds : angle 5.08267 / 3.56 ( 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 91 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.215 Fit side-chains REVERT: A 498 MET cc_start: 0.8106 (mtp) cc_final: 0.7363 (mpp) REVERT: A 608 TYR cc_start: 0.7367 (p90) cc_final: 0.7086 (p90) REVERT: A 613 MET cc_start: 0.6948 (ttt) cc_final: 0.6668 (ptm) REVERT: A 679 TYR cc_start: 0.7445 (t80) cc_final: 0.6863 (t80) REVERT: A 782 ILE cc_start: 0.6130 (OUTLIER) cc_final: 0.5841 (mm) REVERT: A 864 ASP cc_start: 0.6152 (p0) cc_final: 0.5566 (p0) REVERT: A 895 ARG cc_start: 0.8061 (ptp-110) cc_final: 0.7524 (ttm110) outliers start: 14 outliers final: 6 residues processed: 88 average time/residue: 0.0604 time to fit residues: 7.1488 Evaluate side-chains 81 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 430 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 782 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 18 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.189105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.133158 restraints weight = 7811.735| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.11 r_work: 0.3237 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3909 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= 0.169 Angle : 0.596 10.563 9426 Z= 0.311 Chirality : 0.044 0.162 1085 Planarity : 0.004 0.049 1097 Dihedral : 14.505 88.322 1207 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.42 % Favored : 94.31 % Rotamer: Outliers : 1.60 % Allowed : 20.82 % Favored : 77.58 % 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: -0.16 (0.31), residues: 756 helix: 1.92 (0.34), residues: 243 sheet: -0.03 (0.37), residues: 200 loop : -1.86 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 812 TYR 0.012 0.001 TYR A 859 PHE 0.015 0.002 PHE A 758 TRP 0.017 0.001 TRP A 358 HIS 0.011 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 6869) covalent geometry : angle 0.59644 / 0.31 ( 9426) hydrogen bonds : bond 0.04007 / 2.91 ( 285) hydrogen bonds : angle 5.10846 / 3.59 ( 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 86 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.149 Fit side-chains REVERT: A 498 MET cc_start: 0.8026 (mtp) cc_final: 0.7368 (mpp) REVERT: A 608 TYR cc_start: 0.7355 (p90) cc_final: 0.7019 (p90) REVERT: A 613 MET cc_start: 0.6931 (ttt) cc_final: 0.6656 (ptm) REVERT: A 679 TYR cc_start: 0.7407 (t80) cc_final: 0.6816 (t80) REVERT: A 864 ASP cc_start: 0.6255 (p0) cc_final: 0.5808 (p0) REVERT: A 895 ARG cc_start: 0.8061 (ptp-110) cc_final: 0.7518 (ttm110) outliers start: 11 outliers final: 7 residues processed: 83 average time/residue: 0.0714 time to fit residues: 7.8877 Evaluate side-chains 81 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 430 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 30.0000 chunk 65 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.190564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134536 restraints weight = 7813.009| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 3.12 r_work: 0.3257 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6869 Z= 0.128 Angle : 0.570 11.303 9426 Z= 0.299 Chirality : 0.043 0.154 1085 Planarity : 0.004 0.048 1097 Dihedral : 14.498 87.631 1207 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.42 % Favored : 94.31 % Rotamer: Outliers : 1.16 % Allowed : 21.40 % Favored : 77.44 % 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: 244 sheet: 0.04 (0.38), residues: 200 loop : -1.84 (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 425 PHE 0.016 0.002 PHE A 758 TRP 0.016 0.001 TRP A 358 HIS 0.014 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 6869) covalent geometry : angle 0.57046 / 0.30 ( 9426) hydrogen bonds : bond 0.03698 / 2.68 ( 285) hydrogen bonds : angle 5.03061 / 3.52 ( 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 86 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.227 Fit side-chains REVERT: A 498 MET cc_start: 0.8089 (mtp) cc_final: 0.7457 (mpp) REVERT: A 608 TYR cc_start: 0.7352 (p90) cc_final: 0.7021 (p90) REVERT: A 613 MET cc_start: 0.6909 (ttt) cc_final: 0.6633 (ptm) REVERT: A 679 TYR cc_start: 0.7413 (t80) cc_final: 0.6795 (t80) REVERT: A 882 CYS cc_start: 0.8555 (t) cc_final: 0.8167 (m) REVERT: A 895 ARG cc_start: 0.8039 (ptp-110) cc_final: 0.7498 (ttm110) outliers start: 8 outliers final: 8 residues processed: 84 average time/residue: 0.0794 time to fit residues: 8.7670 Evaluate side-chains 86 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 823 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 33 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 65 optimal weight: 0.0570 chunk 36 optimal weight: 0.1980 chunk 48 optimal weight: 0.9980 overall best weight: 0.8300 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.191573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.134930 restraints weight = 7781.532| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.27 r_work: 0.3291 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6869 Z= 0.120 Angle : 0.564 11.314 9426 Z= 0.296 Chirality : 0.043 0.144 1085 Planarity : 0.004 0.048 1097 Dihedral : 14.480 87.005 1207 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.42 % Favored : 94.31 % Rotamer: Outliers : 1.16 % Allowed : 21.40 % Favored : 77.44 % 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: 1.89 (0.34), residues: 247 sheet: 0.08 (0.38), residues: 199 loop : -1.87 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 920 TYR 0.010 0.001 TYR A 425 PHE 0.016 0.002 PHE A 758 TRP 0.015 0.001 TRP A 358 HIS 0.009 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 6869) covalent geometry : angle 0.56386 / 0.30 ( 9426) hydrogen bonds : bond 0.03505 / 2.53 ( 285) hydrogen bonds : angle 4.99118 / 3.49 ( 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: 8 poor density : 81 time to evaluate : 0.162 Fit side-chains REVERT: A 498 MET cc_start: 0.8145 (mtp) cc_final: 0.7546 (mpp) REVERT: A 608 TYR cc_start: 0.7485 (p90) cc_final: 0.7160 (p90) REVERT: A 611 ARG cc_start: 0.8111 (mtp-110) cc_final: 0.7863 (ttm-80) REVERT: A 613 MET cc_start: 0.6901 (ttt) cc_final: 0.6639 (ptm) REVERT: A 679 TYR cc_start: 0.7510 (t80) cc_final: 0.7025 (t80) REVERT: A 882 CYS cc_start: 0.8529 (t) cc_final: 0.8191 (m) REVERT: A 895 ARG cc_start: 0.8069 (ptp-110) cc_final: 0.7533 (ttm110) outliers start: 8 outliers final: 7 residues processed: 86 average time/residue: 0.0731 time to fit residues: 8.3671 Evaluate side-chains 86 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 430 VAL Chi-restraints excluded: chain A residue 622 MET 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: 7.9990 chunk 59 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 GLN A 380 HIS A 801 ASN A 819 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.186823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119940 restraints weight = 7787.846| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.79 r_work: 0.3273 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 6869 Z= 0.252 Angle : 0.657 12.258 9426 Z= 0.342 Chirality : 0.046 0.165 1085 Planarity : 0.005 0.047 1097 Dihedral : 14.463 86.836 1207 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.82 % Favored : 93.92 % Rotamer: Outliers : 1.46 % Allowed : 20.96 % Favored : 77.58 % 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: -0.30 (0.31), residues: 756 helix: 1.81 (0.34), residues: 244 sheet: -0.09 (0.38), residues: 199 loop : -1.97 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 611 TYR 0.017 0.001 TYR A 859 PHE 0.017 0.002 PHE A 320 TRP 0.021 0.002 TRP A 358 HIS 0.014 0.002 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.25 ( 6869) covalent geometry : angle 0.65707 / 0.34 ( 9426) hydrogen bonds : bond 0.04597 / 3.33 ( 285) hydrogen bonds : angle 5.21295 / 3.67 ( 825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1474.31 seconds wall clock time: 25 minutes 59.29 seconds (1559.29 seconds total)