Starting phenix.real_space_refine on Tue Feb 11 18:51:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij0_60611/02_2025/9ij0_60611.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij0_60611/02_2025/9ij0_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_60611/02_2025/9ij0_60611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij0_60611/02_2025/9ij0_60611.map" model { file = "/net/cci-nas-00/data/ceres_data/9ij0_60611/02_2025/9ij0_60611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij0_60611/02_2025/9ij0_60611.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.57, per 1000 atoms: 0.69 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: 1.88 Conformation dependent library (CDL) restraints added in 767.2 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: 2.19 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: 2.59 Time building geometry restraints manager: 2.14 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: 0.250 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 21.010 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 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= 0.340 Angle : 0.846 20.657 9426 Z= 0.450 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.001 TRP A 358 HIS 0.005 0.001 HIS A 353 PHE 0.014 0.002 PHE A 758 TYR 0.010 0.001 TYR A 859 ARG 0.014 0.001 ARG A 652 *********************** 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 : 0.711 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: 0.2517 time to fit residues: 48.1880 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 : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 0.0870 chunk 23 optimal weight: 20.0000 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN A 398 GLN A 539 GLN A 704 GLN A 746 HIS A 825 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.198630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.140713 restraints weight = 7743.787| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.82 r_work: 0.3440 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6869 Z= 0.235 Angle : 0.622 8.226 9426 Z= 0.325 Chirality : 0.045 0.199 1085 Planarity : 0.005 0.062 1097 Dihedral : 14.649 92.358 1207 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.95 % Favored : 93.78 % Rotamer: Outliers : 1.75 % Allowed : 15.43 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.30), residues: 756 helix: 1.84 (0.35), residues: 244 sheet: -0.15 (0.35), residues: 200 loop : -2.11 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 358 HIS 0.002 0.001 HIS A 559 PHE 0.017 0.002 PHE A 758 TYR 0.020 0.001 TYR A 425 ARG 0.004 0.001 ARG A 920 *********************** 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 106 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.713 Fit side-chains REVERT: A 386 ASP cc_start: 0.7175 (m-30) cc_final: 0.6619 (p0) REVERT: A 462 VAL cc_start: 0.7100 (OUTLIER) cc_final: 0.6718 (t) REVERT: A 492 LEU cc_start: 0.7097 (mp) cc_final: 0.6808 (tp) REVERT: A 498 MET cc_start: 0.7804 (mtp) cc_final: 0.7379 (mpp) REVERT: A 613 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.6463 (ptm) REVERT: A 679 TYR cc_start: 0.7800 (t80) cc_final: 0.7085 (t80) outliers start: 12 outliers final: 5 residues processed: 101 average time/residue: 0.1990 time to fit residues: 27.2520 Evaluate side-chains 88 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 462 VAL 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 823 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 1 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 4 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 517 GLN A 819 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.186949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.121067 restraints weight = 7888.923| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.79 r_work: 0.3288 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6869 Z= 0.332 Angle : 0.642 7.736 9426 Z= 0.333 Chirality : 0.046 0.180 1085 Planarity : 0.005 0.058 1097 Dihedral : 14.603 89.887 1207 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.69 % Favored : 94.05 % Rotamer: Outliers : 2.91 % Allowed : 16.89 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.30), residues: 756 helix: 1.72 (0.33), residues: 243 sheet: -0.07 (0.36), residues: 200 loop : -1.92 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 358 HIS 0.004 0.001 HIS A 893 PHE 0.016 0.002 PHE A 320 TYR 0.020 0.002 TYR A 859 ARG 0.005 0.001 ARG A 812 *********************** 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 104 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.727 Fit side-chains REVERT: A 367 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7733 (ptm-80) REVERT: A 498 MET cc_start: 0.8234 (mtp) cc_final: 0.7547 (mpp) REVERT: A 613 MET cc_start: 0.7194 (ttt) cc_final: 0.6888 (ptm) REVERT: A 679 TYR cc_start: 0.7427 (t80) cc_final: 0.7095 (t80) outliers start: 20 outliers final: 9 residues processed: 99 average time/residue: 0.2062 time to fit residues: 27.0691 Evaluate side-chains 82 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 418 THR 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 823 VAL Chi-restraints excluded: chain A residue 873 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 15 optimal weight: 0.0570 chunk 12 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A 819 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.189564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124198 restraints weight = 7928.362| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.78 r_work: 0.3321 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6869 Z= 0.218 Angle : 0.565 7.301 9426 Z= 0.294 Chirality : 0.044 0.226 1085 Planarity : 0.004 0.055 1097 Dihedral : 14.457 86.909 1207 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.82 % Favored : 93.92 % Rotamer: Outliers : 2.18 % Allowed : 17.61 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.31), residues: 756 helix: 1.83 (0.34), residues: 244 sheet: 0.08 (0.37), residues: 200 loop : -1.91 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 358 HIS 0.003 0.001 HIS A 893 PHE 0.017 0.002 PHE A 603 TYR 0.012 0.001 TYR A 425 ARG 0.002 0.000 ARG A 354 *********************** 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 102 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.715 Fit side-chains REVERT: A 493 PRO cc_start: 0.8418 (Cg_exo) cc_final: 0.7994 (Cg_endo) REVERT: A 498 MET cc_start: 0.8082 (mtp) cc_final: 0.7514 (mpp) REVERT: A 501 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8440 (mt) REVERT: A 613 MET cc_start: 0.7126 (ttt) cc_final: 0.6792 (ptm) REVERT: A 679 TYR cc_start: 0.7398 (t80) cc_final: 0.6836 (t80) REVERT: A 928 MET cc_start: 0.8733 (mtp) cc_final: 0.8441 (mtp) outliers start: 15 outliers final: 9 residues processed: 97 average time/residue: 0.1965 time to fit residues: 25.3043 Evaluate side-chains 90 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 501 ILE 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 823 VAL Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 895 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 31 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A 819 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.186665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.120332 restraints weight = 7876.656| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.79 r_work: 0.3276 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6869 Z= 0.346 Angle : 0.639 10.657 9426 Z= 0.324 Chirality : 0.045 0.196 1085 Planarity : 0.005 0.052 1097 Dihedral : 14.419 87.008 1207 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.29 % Favored : 94.44 % Rotamer: Outliers : 2.04 % Allowed : 19.07 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.31), residues: 756 helix: 1.72 (0.34), residues: 245 sheet: 0.02 (0.37), residues: 200 loop : -2.02 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 358 HIS 0.004 0.001 HIS A 892 PHE 0.017 0.002 PHE A 320 TYR 0.018 0.001 TYR A 859 ARG 0.003 0.000 ARG A 367 *********************** 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 98 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.684 Fit side-chains REVERT: A 384 ARG cc_start: 0.6881 (mtt90) cc_final: 0.6417 (mtt90) REVERT: A 498 MET cc_start: 0.8110 (mtp) cc_final: 0.7493 (mpp) REVERT: A 501 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8437 (mt) REVERT: A 679 TYR cc_start: 0.7470 (t80) cc_final: 0.6941 (t80) outliers start: 14 outliers final: 8 residues processed: 93 average time/residue: 0.2146 time to fit residues: 26.2165 Evaluate side-chains 87 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 501 ILE 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 823 VAL Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 895 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 25 optimal weight: 4.9990 chunk 13 optimal weight: 0.0060 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN 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 = 0.191095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.124954 restraints weight = 7797.716| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.80 r_work: 0.3335 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6869 Z= 0.167 Angle : 0.551 9.839 9426 Z= 0.280 Chirality : 0.043 0.178 1085 Planarity : 0.004 0.048 1097 Dihedral : 14.226 84.737 1207 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.76 % Favored : 94.97 % Rotamer: Outliers : 1.31 % Allowed : 20.23 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.31), residues: 756 helix: 1.86 (0.34), residues: 247 sheet: 0.13 (0.37), residues: 200 loop : -1.94 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 358 HIS 0.002 0.001 HIS A 927 PHE 0.018 0.002 PHE A 603 TYR 0.009 0.001 TYR A 770 ARG 0.002 0.000 ARG A 920 *********************** 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 98 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.681 Fit side-chains REVERT: A 384 ARG cc_start: 0.6916 (mtt90) cc_final: 0.6472 (mtt90) REVERT: A 389 LEU cc_start: 0.6839 (mt) cc_final: 0.6251 (tp) REVERT: A 425 TYR cc_start: 0.6262 (m-80) cc_final: 0.5959 (m-80) REVERT: A 493 PRO cc_start: 0.8398 (Cg_endo) cc_final: 0.8039 (Cg_exo) REVERT: A 498 MET cc_start: 0.8091 (mtp) cc_final: 0.7497 (mpp) REVERT: A 501 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8367 (mt) REVERT: A 603 PHE cc_start: 0.8286 (m-80) cc_final: 0.8063 (m-10) REVERT: A 679 TYR cc_start: 0.7429 (t80) cc_final: 0.7010 (t80) REVERT: A 864 ASP cc_start: 0.6004 (p0) cc_final: 0.5490 (p0) outliers start: 9 outliers final: 4 residues processed: 92 average time/residue: 0.2114 time to fit residues: 25.6410 Evaluate side-chains 83 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 622 MET 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 44 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 0.0070 chunk 53 optimal weight: 9.9990 overall best weight: 1.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 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 = 0.4140 r_free = 0.4140 target = 0.189833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.132306 restraints weight = 7727.354| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.17 r_work: 0.3259 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6869 Z= 0.216 Angle : 0.567 8.659 9426 Z= 0.290 Chirality : 0.043 0.152 1085 Planarity : 0.004 0.046 1097 Dihedral : 14.133 83.793 1207 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.16 % Favored : 94.58 % Rotamer: Outliers : 1.02 % Allowed : 20.96 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.31), residues: 756 helix: 1.95 (0.35), residues: 247 sheet: 0.15 (0.37), residues: 199 loop : -1.99 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 358 HIS 0.003 0.001 HIS A 903 PHE 0.016 0.002 PHE A 603 TYR 0.013 0.001 TYR A 859 ARG 0.002 0.000 ARG A 920 *********************** 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: 7 poor density : 84 time to evaluate : 0.695 Fit side-chains REVERT: A 384 ARG cc_start: 0.6925 (mtt90) cc_final: 0.6511 (mtt90) REVERT: A 425 TYR cc_start: 0.6429 (m-80) cc_final: 0.6149 (m-80) REVERT: A 498 MET cc_start: 0.8253 (mtp) cc_final: 0.7582 (mpp) REVERT: A 501 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8224 (mt) REVERT: A 603 PHE cc_start: 0.8340 (m-80) cc_final: 0.8089 (m-10) REVERT: A 782 ILE cc_start: 0.6368 (OUTLIER) cc_final: 0.6114 (mt) REVERT: A 882 CYS cc_start: 0.8423 (t) cc_final: 0.8189 (m) REVERT: A 895 ARG cc_start: 0.8010 (ptp-110) cc_final: 0.7620 (ttm-80) outliers start: 7 outliers final: 5 residues processed: 89 average time/residue: 0.1951 time to fit residues: 23.1790 Evaluate side-chains 85 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 873 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 31 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 72 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.190859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.124570 restraints weight = 7760.739| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.79 r_work: 0.3328 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6869 Z= 0.194 Angle : 0.562 8.915 9426 Z= 0.284 Chirality : 0.043 0.141 1085 Planarity : 0.004 0.046 1097 Dihedral : 14.053 82.849 1207 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.29 % Favored : 94.44 % Rotamer: Outliers : 1.16 % Allowed : 21.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.31), residues: 756 helix: 1.94 (0.34), residues: 249 sheet: 0.21 (0.38), residues: 198 loop : -1.99 (0.31), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 358 HIS 0.002 0.001 HIS A 903 PHE 0.015 0.002 PHE A 758 TYR 0.010 0.001 TYR A 859 ARG 0.002 0.000 ARG A 812 *********************** 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 89 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.631 Fit side-chains REVERT: A 329 MET cc_start: 0.7943 (ttm) cc_final: 0.7357 (ttm) REVERT: A 384 ARG cc_start: 0.6841 (mtt90) cc_final: 0.6468 (mtt90) REVERT: A 425 TYR cc_start: 0.6391 (m-80) cc_final: 0.6130 (m-80) REVERT: A 493 PRO cc_start: 0.8446 (Cg_exo) cc_final: 0.8156 (Cg_endo) REVERT: A 498 MET cc_start: 0.8229 (mtp) cc_final: 0.7569 (mpp) REVERT: A 501 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8185 (mt) REVERT: A 518 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7348 (mp10) REVERT: A 603 PHE cc_start: 0.8269 (m-80) cc_final: 0.8047 (m-10) REVERT: A 679 TYR cc_start: 0.7429 (t80) cc_final: 0.7122 (t80) REVERT: A 895 ARG cc_start: 0.8024 (ptp-110) cc_final: 0.7630 (ttm-80) outliers start: 8 outliers final: 6 residues processed: 86 average time/residue: 0.2211 time to fit residues: 25.0255 Evaluate side-chains 87 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 501 ILE 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 873 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 56 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS 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 = 0.4118 r_free = 0.4118 target = 0.187705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.121783 restraints weight = 7894.489| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.78 r_work: 0.3293 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6869 Z= 0.286 Angle : 0.601 8.915 9426 Z= 0.304 Chirality : 0.044 0.140 1085 Planarity : 0.004 0.045 1097 Dihedral : 14.028 82.559 1207 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.82 % Favored : 93.92 % Rotamer: Outliers : 1.46 % Allowed : 20.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.31), residues: 756 helix: 1.95 (0.34), residues: 246 sheet: -0.02 (0.37), residues: 205 loop : -2.00 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 358 HIS 0.004 0.001 HIS A 903 PHE 0.018 0.002 PHE A 320 TYR 0.016 0.001 TYR A 859 ARG 0.006 0.000 ARG A 611 *********************** 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 90 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.724 Fit side-chains REVERT: A 384 ARG cc_start: 0.6984 (mtt90) cc_final: 0.6689 (mtt90) REVERT: A 425 TYR cc_start: 0.6531 (m-80) cc_final: 0.6263 (m-80) REVERT: A 493 PRO cc_start: 0.8614 (Cg_exo) cc_final: 0.8248 (Cg_endo) REVERT: A 498 MET cc_start: 0.8276 (mtp) cc_final: 0.7583 (mpp) REVERT: A 501 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8208 (mt) REVERT: A 632 MET cc_start: 0.8159 (ttt) cc_final: 0.7662 (ttt) REVERT: A 679 TYR cc_start: 0.7494 (t80) cc_final: 0.7082 (t80) outliers start: 10 outliers final: 9 residues processed: 86 average time/residue: 0.2035 time to fit residues: 23.4905 Evaluate side-chains 88 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 430 VAL Chi-restraints excluded: chain A residue 501 ILE 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 823 VAL Chi-restraints excluded: chain A residue 873 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 0.0970 chunk 16 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 0.3980 chunk 29 optimal weight: 6.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 819 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.188415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.131289 restraints weight = 7994.815| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.16 r_work: 0.3251 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6869 Z= 0.261 Angle : 0.591 11.280 9426 Z= 0.299 Chirality : 0.044 0.233 1085 Planarity : 0.004 0.045 1097 Dihedral : 13.973 82.095 1207 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.29 % Favored : 94.44 % Rotamer: Outliers : 1.60 % Allowed : 20.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.31), residues: 756 helix: 1.94 (0.34), residues: 247 sheet: 0.15 (0.37), residues: 198 loop : -2.06 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 358 HIS 0.003 0.001 HIS A 892 PHE 0.016 0.002 PHE A 320 TYR 0.014 0.001 TYR A 859 ARG 0.003 0.000 ARG A 611 ********************** 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 90 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.727 Fit side-chains REVERT: A 329 MET cc_start: 0.8103 (ttm) cc_final: 0.7540 (ttm) REVERT: A 384 ARG cc_start: 0.7081 (mtt90) cc_final: 0.6813 (mtt90) REVERT: A 493 PRO cc_start: 0.8575 (Cg_exo) cc_final: 0.8274 (Cg_endo) REVERT: A 498 MET cc_start: 0.8396 (mtp) cc_final: 0.7717 (mpp) REVERT: A 501 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8209 (mt) REVERT: A 510 ARG cc_start: 0.7961 (mpt180) cc_final: 0.7734 (mpt180) REVERT: A 679 TYR cc_start: 0.7595 (t80) cc_final: 0.7301 (t80) outliers start: 11 outliers final: 10 residues processed: 86 average time/residue: 0.2135 time to fit residues: 24.3511 Evaluate side-chains 90 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 501 ILE 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 823 VAL Chi-restraints excluded: chain A residue 873 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.191364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.124844 restraints weight = 7886.616| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.81 r_work: 0.3327 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6869 Z= 0.180 Angle : 0.554 10.286 9426 Z= 0.280 Chirality : 0.042 0.167 1085 Planarity : 0.004 0.045 1097 Dihedral : 13.900 81.390 1207 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.42 % Favored : 94.44 % Rotamer: Outliers : 1.46 % Allowed : 21.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.31), residues: 756 helix: 2.00 (0.34), residues: 248 sheet: -0.01 (0.37), residues: 205 loop : -2.00 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 358 HIS 0.004 0.001 HIS A 393 PHE 0.017 0.001 PHE A 758 TYR 0.009 0.001 TYR A 770 ARG 0.002 0.000 ARG A 920 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3538.34 seconds wall clock time: 63 minutes 18.68 seconds (3798.68 seconds total)