Starting phenix.real_space_refine on Wed Sep 17 07:02:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij0_60611/09_2025/9ij0_60611.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij0_60611/09_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_60611/09_2025/9ij0_60611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij0_60611/09_2025/9ij0_60611.map" model { file = "/net/cci-nas-00/data/ceres_data/9ij0_60611/09_2025/9ij0_60611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij0_60611/09_2025/9ij0_60611.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.167 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 27 5.49 5 Mg 2 5.21 5 S 45 5.16 5 C 4156 2.51 5 N 1161 2.21 5 O 1276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 1.80, per 1000 atoms: 0.27 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: 0.64 Conformation dependent library (CDL) restraints added in 350.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.85 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: 1.31 Time building geometry restraints manager: 0.87 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.280 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.410 ------------------------------------------------------------------------------- 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= 0.291 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00579 ( 6869) covalent geometry : angle 0.84647 ( 9426) hydrogen bonds : bond 0.15826 ( 285) hydrogen bonds : angle 7.23593 ( 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 : 0.297 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: 0.1258 time to fit residues: 23.9300 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 : 0.192 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 234 HIS 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 = 0.4100 r_free = 0.4100 target = 0.185644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131508 restraints weight = 7904.447| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.20 r_work: 0.3220 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 6869 Z= 0.298 Angle : 0.744 8.309 9426 Z= 0.386 Chirality : 0.050 0.225 1085 Planarity : 0.006 0.061 1097 Dihedral : 14.663 92.809 1207 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.75 % Favored : 92.99 % Rotamer: Outliers : 2.47 % Allowed : 15.14 % Favored : 82.39 % 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 aren not related in a simple way. whole: -0.73 (0.30), residues: 756 helix: 1.43 (0.33), residues: 243 sheet: -0.41 (0.35), residues: 203 loop : -2.14 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 700 TYR 0.026 0.002 TYR A 859 PHE 0.020 0.003 PHE A 341 TRP 0.033 0.003 TRP A 358 HIS 0.006 0.002 HIS A 893 Details of bonding type rmsd covalent geometry : bond 0.00723 ( 6869) covalent geometry : angle 0.74434 ( 9426) hydrogen bonds : bond 0.05501 ( 285) hydrogen bonds : angle 5.67509 ( 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 107 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.255 Fit side-chains REVERT: A 462 VAL cc_start: 0.6875 (OUTLIER) cc_final: 0.6445 (t) REVERT: A 492 LEU cc_start: 0.6983 (mp) cc_final: 0.6555 (tp) REVERT: A 498 MET cc_start: 0.7997 (mtp) cc_final: 0.7320 (mpp) REVERT: A 583 ASP cc_start: 0.7934 (t0) cc_final: 0.7712 (m-30) REVERT: A 608 TYR cc_start: 0.7559 (p90) cc_final: 0.7303 (p90) REVERT: A 613 MET cc_start: 0.6949 (ttt) cc_final: 0.6555 (ptm) REVERT: A 622 MET cc_start: 0.6894 (tpp) cc_final: 0.6671 (tpp) REVERT: A 679 TYR cc_start: 0.7547 (t80) cc_final: 0.7070 (t80) outliers start: 17 outliers final: 11 residues processed: 99 average time/residue: 0.0811 time to fit residues: 10.7620 Evaluate side-chains 90 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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 277 LEU 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 598 THR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 873 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 472 HIS A 517 GLN A 540 ASN A 819 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.191063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.125176 restraints weight = 7718.233| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.77 r_work: 0.3340 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3525 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= 0.126 Angle : 0.570 7.879 9426 Z= 0.297 Chirality : 0.044 0.194 1085 Planarity : 0.004 0.059 1097 Dihedral : 14.608 89.349 1207 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.16 % Favored : 94.58 % Rotamer: Outliers : 2.33 % Allowed : 16.59 % Favored : 81.08 % 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 aren not related in a simple way. whole: -0.27 (0.30), residues: 756 helix: 1.80 (0.34), residues: 244 sheet: -0.03 (0.36), residues: 200 loop : -1.95 (0.31), 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 603 TRP 0.017 0.001 TRP A 358 HIS 0.002 0.001 HIS A 893 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6869) covalent geometry : angle 0.57038 ( 9426) hydrogen bonds : bond 0.03713 ( 285) hydrogen bonds : angle 5.19960 ( 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 99 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.252 Fit side-chains REVERT: A 498 MET cc_start: 0.8205 (mtp) cc_final: 0.7530 (mpp) REVERT: A 608 TYR cc_start: 0.7438 (p90) cc_final: 0.7151 (p90) REVERT: A 613 MET cc_start: 0.6723 (ttt) cc_final: 0.6373 (ptm) REVERT: A 622 MET cc_start: 0.7064 (tpp) cc_final: 0.6774 (tpp) REVERT: A 679 TYR cc_start: 0.7456 (t80) cc_final: 0.6830 (t80) REVERT: A 928 MET cc_start: 0.8698 (mtp) cc_final: 0.8356 (mtp) REVERT: A 954 GLN cc_start: 0.7831 (tp40) cc_final: 0.7538 (tp40) outliers start: 16 outliers final: 5 residues processed: 95 average time/residue: 0.0776 time to fit residues: 9.9325 Evaluate side-chains 81 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 791 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.0470 chunk 75 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 overall best weight: 2.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4110 r_free = 0.4110 target = 0.186564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.128944 restraints weight = 7963.137| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.16 r_work: 0.3208 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3981 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= 0.215 Angle : 0.626 11.931 9426 Z= 0.323 Chirality : 0.045 0.168 1085 Planarity : 0.005 0.053 1097 Dihedral : 14.514 87.985 1207 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.29 % Favored : 94.44 % Rotamer: Outliers : 2.62 % Allowed : 18.20 % Favored : 79.18 % 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 aren not related in a simple way. whole: -0.35 (0.30), residues: 756 helix: 1.74 (0.34), residues: 243 sheet: -0.04 (0.37), residues: 200 loop : -2.03 (0.31), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 536 TYR 0.018 0.001 TYR A 859 PHE 0.016 0.002 PHE A 320 TRP 0.023 0.002 TRP A 358 HIS 0.005 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 6869) covalent geometry : angle 0.62643 ( 9426) hydrogen bonds : bond 0.04661 ( 285) hydrogen bonds : angle 5.28303 ( 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 96 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.229 Fit side-chains REVERT: A 384 ARG cc_start: 0.6749 (mtt90) cc_final: 0.6337 (mtt90) REVERT: A 498 MET cc_start: 0.8181 (mtp) cc_final: 0.7619 (mpp) REVERT: A 501 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8458 (mt) REVERT: A 608 TYR cc_start: 0.7601 (p90) cc_final: 0.6790 (p90) REVERT: A 622 MET cc_start: 0.7066 (tpp) cc_final: 0.6756 (tpp) REVERT: A 679 TYR cc_start: 0.7428 (t80) cc_final: 0.6799 (t80) outliers start: 18 outliers final: 8 residues processed: 91 average time/residue: 0.0875 time to fit residues: 10.5622 Evaluate side-chains 84 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 823 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 353 HIS A 819 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.186297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.129826 restraints weight = 8018.094| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.22 r_work: 0.3213 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6869 Z= 0.212 Angle : 0.612 9.411 9426 Z= 0.318 Chirality : 0.045 0.165 1085 Planarity : 0.005 0.051 1097 Dihedral : 14.366 86.050 1207 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.16 % Favored : 94.58 % Rotamer: Outliers : 2.77 % Allowed : 19.51 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.30), residues: 756 helix: 1.69 (0.34), residues: 245 sheet: -0.13 (0.37), residues: 200 loop : -2.05 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 812 TYR 0.017 0.001 TYR A 859 PHE 0.015 0.002 PHE A 320 TRP 0.022 0.002 TRP A 358 HIS 0.004 0.001 HIS A 893 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 6869) covalent geometry : angle 0.61220 ( 9426) hydrogen bonds : bond 0.04479 ( 285) hydrogen bonds : angle 5.22461 ( 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 104 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.247 Fit side-chains REVERT: A 384 ARG cc_start: 0.6948 (mtt90) cc_final: 0.6557 (mtt90) REVERT: A 494 GLU cc_start: 0.8491 (tt0) cc_final: 0.8180 (pt0) REVERT: A 498 MET cc_start: 0.8205 (mtp) cc_final: 0.7536 (mpp) REVERT: A 501 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8461 (mt) REVERT: A 510 ARG cc_start: 0.8041 (mpt180) cc_final: 0.7822 (mpt180) REVERT: A 608 TYR cc_start: 0.7695 (p90) cc_final: 0.7159 (p90) REVERT: A 613 MET cc_start: 0.7218 (ttt) cc_final: 0.6856 (ptm) REVERT: A 622 MET cc_start: 0.7201 (tpp) cc_final: 0.6900 (tpp) REVERT: A 679 TYR cc_start: 0.7482 (t80) cc_final: 0.7064 (t80) REVERT: A 782 ILE cc_start: 0.6374 (OUTLIER) cc_final: 0.6122 (mt) REVERT: A 895 ARG cc_start: 0.8049 (ptp-110) cc_final: 0.7536 (ttm110) REVERT: A 954 GLN cc_start: 0.7716 (tp40) cc_final: 0.7420 (tp40) outliers start: 19 outliers final: 11 residues processed: 100 average time/residue: 0.0979 time to fit residues: 12.7761 Evaluate side-chains 92 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ARG 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 501 ILE Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 873 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 50 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.188758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.131863 restraints weight = 7973.686| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.40 r_work: 0.3254 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6869 Z= 0.139 Angle : 0.577 10.137 9426 Z= 0.296 Chirality : 0.044 0.260 1085 Planarity : 0.004 0.047 1097 Dihedral : 14.241 85.118 1207 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.69 % Favored : 94.05 % Rotamer: Outliers : 2.04 % Allowed : 21.11 % Favored : 76.86 % 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 aren not related in a simple way. whole: -0.21 (0.31), residues: 756 helix: 1.91 (0.34), residues: 245 sheet: 0.02 (0.37), residues: 200 loop : -2.01 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 611 TYR 0.010 0.001 TYR A 859 PHE 0.016 0.002 PHE A 758 TRP 0.016 0.001 TRP A 358 HIS 0.005 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6869) covalent geometry : angle 0.57652 ( 9426) hydrogen bonds : bond 0.03797 ( 285) hydrogen bonds : angle 4.98139 ( 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 99 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.243 Fit side-chains REVERT: A 384 ARG cc_start: 0.7082 (mtt90) cc_final: 0.6699 (mtt90) REVERT: A 498 MET cc_start: 0.8228 (mtp) cc_final: 0.7597 (mpp) REVERT: A 501 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8226 (mt) REVERT: A 608 TYR cc_start: 0.7763 (p90) cc_final: 0.7246 (p90) REVERT: A 613 MET cc_start: 0.7156 (ttt) cc_final: 0.6802 (ptm) REVERT: A 622 MET cc_start: 0.7025 (tpp) cc_final: 0.6745 (tpp) REVERT: A 782 ILE cc_start: 0.6414 (OUTLIER) cc_final: 0.6161 (mt) REVERT: A 895 ARG cc_start: 0.7912 (ptp-110) cc_final: 0.7355 (ttm110) REVERT: A 954 GLN cc_start: 0.7833 (tp40) cc_final: 0.7567 (tp40) outliers start: 14 outliers final: 9 residues processed: 96 average time/residue: 0.0957 time to fit residues: 11.9829 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 : 0.266 ------------------------------------------------------------------------------- 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 553 SER Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 873 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 57 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 72 optimal weight: 0.0570 chunk 34 optimal weight: 7.9990 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 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 = 0.4114 r_free = 0.4114 target = 0.187172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.130650 restraints weight = 7824.962| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.20 r_work: 0.3252 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.4698 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= 0.158 Angle : 0.606 11.511 9426 Z= 0.305 Chirality : 0.045 0.253 1085 Planarity : 0.004 0.051 1097 Dihedral : 14.158 84.008 1207 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.42 % Favored : 94.31 % Rotamer: Outliers : 2.04 % Allowed : 21.11 % Favored : 76.86 % 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 aren not related in a simple way. whole: -0.20 (0.30), residues: 756 helix: 1.95 (0.34), residues: 245 sheet: 0.08 (0.37), residues: 198 loop : -2.06 (0.30), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 920 TYR 0.012 0.001 TYR A 859 PHE 0.015 0.002 PHE A 758 TRP 0.018 0.001 TRP A 358 HIS 0.005 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 6869) covalent geometry : angle 0.60634 ( 9426) hydrogen bonds : bond 0.03984 ( 285) hydrogen bonds : angle 5.00811 ( 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 94 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.248 Fit side-chains REVERT: A 384 ARG cc_start: 0.7060 (mtt90) cc_final: 0.6714 (mtt90) REVERT: A 498 MET cc_start: 0.8363 (mtp) cc_final: 0.7632 (mpp) REVERT: A 501 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8288 (mt) REVERT: A 608 TYR cc_start: 0.7755 (p90) cc_final: 0.7272 (p90) REVERT: A 613 MET cc_start: 0.7104 (ttt) cc_final: 0.6748 (ptm) REVERT: A 622 MET cc_start: 0.7037 (tpp) cc_final: 0.6715 (tpp) REVERT: A 752 MET cc_start: 0.3600 (mmt) cc_final: 0.3343 (mmp) outliers start: 14 outliers final: 10 residues processed: 90 average time/residue: 0.0932 time to fit residues: 11.0885 Evaluate side-chains 89 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 553 SER Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 873 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 18 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.184308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.129999 restraints weight = 7968.017| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.88 r_work: 0.3229 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6869 Z= 0.239 Angle : 0.663 8.581 9426 Z= 0.337 Chirality : 0.048 0.233 1085 Planarity : 0.005 0.047 1097 Dihedral : 14.205 83.886 1207 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.82 % Favored : 93.92 % Rotamer: Outliers : 2.33 % Allowed : 21.11 % Favored : 76.56 % 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 aren not related in a simple way. whole: -0.45 (0.30), residues: 756 helix: 1.77 (0.34), residues: 245 sheet: -0.19 (0.36), residues: 203 loop : -2.16 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 536 TYR 0.018 0.001 TYR A 859 PHE 0.018 0.002 PHE A 320 TRP 0.023 0.002 TRP A 358 HIS 0.005 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00588 ( 6869) covalent geometry : angle 0.66305 ( 9426) hydrogen bonds : bond 0.04724 ( 285) hydrogen bonds : angle 5.16807 ( 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 93 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.247 Fit side-chains REVERT: A 498 MET cc_start: 0.8598 (mtp) cc_final: 0.7936 (mpp) REVERT: A 501 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8625 (mt) REVERT: A 603 PHE cc_start: 0.8520 (m-80) cc_final: 0.8167 (m-10) REVERT: A 622 MET cc_start: 0.7266 (tpp) cc_final: 0.6972 (tpp) REVERT: A 632 MET cc_start: 0.8312 (ttt) cc_final: 0.7789 (ttt) REVERT: A 679 TYR cc_start: 0.7800 (t80) cc_final: 0.7475 (t80) REVERT: A 752 MET cc_start: 0.3861 (mmt) cc_final: 0.3632 (mmp) outliers start: 16 outliers final: 10 residues processed: 90 average time/residue: 0.0857 time to fit residues: 10.4636 Evaluate side-chains 83 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 553 SER 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 868 THR Chi-restraints excluded: chain A residue 873 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 28 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.186282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.132307 restraints weight = 7956.361| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.80 r_work: 0.3261 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6869 Z= 0.168 Angle : 0.608 8.899 9426 Z= 0.309 Chirality : 0.045 0.216 1085 Planarity : 0.004 0.045 1097 Dihedral : 14.108 83.145 1207 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.69 % Favored : 94.05 % Rotamer: Outliers : 1.75 % Allowed : 20.96 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.30), residues: 756 helix: 1.91 (0.34), residues: 246 sheet: -0.19 (0.36), residues: 204 loop : -2.12 (0.31), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 384 TYR 0.011 0.001 TYR A 859 PHE 0.016 0.002 PHE A 758 TRP 0.018 0.001 TRP A 358 HIS 0.005 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 6869) covalent geometry : angle 0.60793 ( 9426) hydrogen bonds : bond 0.04070 ( 285) hydrogen bonds : angle 5.03225 ( 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 89 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.240 Fit side-chains REVERT: A 329 MET cc_start: 0.8417 (ttm) cc_final: 0.7947 (ttm) REVERT: A 425 TYR cc_start: 0.7165 (m-80) cc_final: 0.6826 (m-80) REVERT: A 483 MET cc_start: -0.1396 (ttp) cc_final: -0.1627 (ppp) REVERT: A 498 MET cc_start: 0.8465 (mtp) cc_final: 0.7870 (mpp) REVERT: A 501 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8542 (mt) REVERT: A 603 PHE cc_start: 0.8533 (m-80) cc_final: 0.8164 (m-10) REVERT: A 608 TYR cc_start: 0.8066 (p90) cc_final: 0.7640 (p90) REVERT: A 622 MET cc_start: 0.7296 (tpp) cc_final: 0.6963 (tpp) REVERT: A 672 MET cc_start: 0.7667 (ttm) cc_final: 0.7306 (mmm) REVERT: A 679 TYR cc_start: 0.7732 (t80) cc_final: 0.7527 (t80) outliers start: 12 outliers final: 11 residues processed: 86 average time/residue: 0.0771 time to fit residues: 9.1926 Evaluate side-chains 88 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 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 555 HIS 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 868 THR 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 33 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 36 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.187530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.134794 restraints weight = 7917.716| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.91 r_work: 0.3267 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6869 Z= 0.144 Angle : 0.601 11.344 9426 Z= 0.301 Chirality : 0.045 0.245 1085 Planarity : 0.004 0.044 1097 Dihedral : 14.051 82.388 1207 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.42 % Favored : 94.31 % Rotamer: Outliers : 2.04 % Allowed : 21.25 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.31), residues: 756 helix: 1.98 (0.34), residues: 247 sheet: -0.10 (0.36), residues: 206 loop : -2.17 (0.31), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 384 TYR 0.011 0.001 TYR A 425 PHE 0.019 0.002 PHE A 758 TRP 0.016 0.001 TRP A 358 HIS 0.004 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6869) covalent geometry : angle 0.60130 ( 9426) hydrogen bonds : bond 0.03823 ( 285) hydrogen bonds : angle 4.95895 ( 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 93 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.254 Fit side-chains REVERT: A 329 MET cc_start: 0.8389 (ttm) cc_final: 0.7921 (ttm) REVERT: A 425 TYR cc_start: 0.7106 (m-80) cc_final: 0.6783 (m-80) REVERT: A 498 MET cc_start: 0.8519 (mtp) cc_final: 0.7917 (mpp) REVERT: A 501 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8416 (mt) REVERT: A 603 PHE cc_start: 0.8545 (m-80) cc_final: 0.8180 (m-10) REVERT: A 608 TYR cc_start: 0.8061 (p90) cc_final: 0.7664 (p90) REVERT: A 622 MET cc_start: 0.7288 (tpp) cc_final: 0.6935 (tpp) REVERT: A 672 MET cc_start: 0.7715 (ttm) cc_final: 0.7439 (mmm) REVERT: A 679 TYR cc_start: 0.7714 (t80) cc_final: 0.7509 (t80) REVERT: A 954 GLN cc_start: 0.8061 (tp40) cc_final: 0.7682 (tt0) outliers start: 14 outliers final: 10 residues processed: 89 average time/residue: 0.0904 time to fit residues: 10.8065 Evaluate side-chains 88 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 555 HIS 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 868 THR 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 57 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.184602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.130177 restraints weight = 7875.823| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.90 r_work: 0.3226 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6869 Z= 0.213 Angle : 0.657 12.669 9426 Z= 0.329 Chirality : 0.047 0.236 1085 Planarity : 0.005 0.044 1097 Dihedral : 14.007 83.625 1207 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.48 % Favored : 93.39 % Rotamer: Outliers : 1.75 % Allowed : 21.54 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.30), residues: 756 helix: 1.83 (0.34), residues: 246 sheet: -0.18 (0.36), residues: 206 loop : -2.29 (0.31), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 611 TYR 0.018 0.002 TYR A 859 PHE 0.016 0.002 PHE A 320 TRP 0.021 0.002 TRP A 358 HIS 0.005 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 6869) covalent geometry : angle 0.65657 ( 9426) hydrogen bonds : bond 0.04542 ( 285) hydrogen bonds : angle 5.10990 ( 825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1828.74 seconds wall clock time: 32 minutes 2.08 seconds (1922.08 seconds total)