Starting phenix.real_space_refine on Fri Dec 27 19:11:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ij0_60611/12_2024/9ij0_60611.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ij0_60611/12_2024/9ij0_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_60611/12_2024/9ij0_60611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ij0_60611/12_2024/9ij0_60611.map" model { file = "/net/cci-nas-00/data/ceres_data/9ij0_60611/12_2024/9ij0_60611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ij0_60611/12_2024/9ij0_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-5532/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: 4.46, per 1000 atoms: 0.67 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: 1.89 Conformation dependent library (CDL) restraints added in 751.7 milliseconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1434 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 34.3% alpha, 25.3% beta 3 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 2.23 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: 2.73 Time building geometry restraints manager: 2.16 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: 0.160 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 21.280 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.860 ------------------------------------------------------------------------------- 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 : 0.730 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: 0.2626 time to fit residues: 50.4707 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 : 0.648 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 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 : 0.667 Fit side-chains REVERT: A 471 ILE cc_start: 0.6360 (OUTLIER) cc_final: 0.6076 (mt) REVERT: A 679 TYR cc_start: 0.7320 (t80) cc_final: 0.6918 (t80) outliers start: 12 outliers final: 5 residues processed: 101 average time/residue: 0.1876 time to fit residues: 25.3585 Evaluate side-chains 87 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 471 ILE 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 38 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 6869 Z= 0.447 Angle : 0.709 8.010 9426 Z= 0.367 Chirality : 0.048 0.196 1085 Planarity : 0.005 0.057 1097 Dihedral : 14.695 91.155 1207 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.69 % Favored : 94.05 % Rotamer: Outliers : 3.49 % Allowed : 16.30 % 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: -0.46 (0.30), residues: 756 helix: 1.60 (0.33), residues: 243 sheet: -0.19 (0.36), residues: 198 loop : -1.97 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 358 HIS 0.005 0.002 HIS A 893 PHE 0.018 0.003 PHE A 320 TYR 0.023 0.002 TYR A 859 ARG 0.004 0.001 ARG A 536 *********************** 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 106 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.805 Fit side-chains REVERT: A 255 ARG cc_start: 0.8192 (ttm110) cc_final: 0.7791 (ttm170) REVERT: A 367 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7502 (ptm-80) REVERT: A 471 ILE cc_start: 0.6328 (OUTLIER) cc_final: 0.6010 (mt) REVERT: A 512 MET cc_start: 0.7501 (mmm) cc_final: 0.7294 (tpp) outliers start: 24 outliers final: 12 residues processed: 99 average time/residue: 0.2035 time to fit residues: 26.6059 Evaluate side-chains 86 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 471 ILE Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 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 68 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6869 Z= 0.174 Angle : 0.560 8.699 9426 Z= 0.292 Chirality : 0.043 0.178 1085 Planarity : 0.004 0.057 1097 Dihedral : 14.508 87.169 1207 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.16 % Favored : 94.58 % Rotamer: Outliers : 2.04 % Allowed : 18.20 % Favored : 79.77 % 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: -0.15 (0.31), residues: 756 helix: 1.86 (0.34), residues: 244 sheet: 0.06 (0.37), residues: 199 loop : -1.86 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 358 HIS 0.002 0.001 HIS A 527 PHE 0.016 0.002 PHE A 758 TYR 0.012 0.001 TYR A 425 ARG 0.003 0.000 ARG A 611 *********************** 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: 14 poor density : 88 time to evaluate : 0.985 Fit side-chains REVERT: A 471 ILE cc_start: 0.6221 (OUTLIER) cc_final: 0.5788 (mt) REVERT: A 865 HIS cc_start: 0.6017 (OUTLIER) cc_final: 0.5620 (p90) outliers start: 14 outliers final: 4 residues processed: 95 average time/residue: 0.2320 time to fit residues: 28.7581 Evaluate side-chains 81 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 471 ILE Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 865 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 0.0980 chunk 1 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6869 Z= 0.171 Angle : 0.569 9.710 9426 Z= 0.286 Chirality : 0.043 0.190 1085 Planarity : 0.004 0.052 1097 Dihedral : 14.391 85.674 1207 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.03 % Favored : 94.71 % Rotamer: Outliers : 1.31 % Allowed : 18.63 % Favored : 80.06 % 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: -0.04 (0.31), residues: 756 helix: 1.88 (0.34), residues: 247 sheet: 0.15 (0.38), residues: 200 loop : -1.79 (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 353 PHE 0.018 0.002 PHE A 603 TYR 0.010 0.001 TYR A 425 ARG 0.003 0.000 ARG A 920 *********************** 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 97 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.844 Fit side-chains REVERT: A 471 ILE cc_start: 0.6212 (OUTLIER) cc_final: 0.5836 (mt) outliers start: 9 outliers final: 5 residues processed: 93 average time/residue: 0.2192 time to fit residues: 27.1982 Evaluate side-chains 84 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 755 VAL 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 24 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 18 optimal weight: 0.0270 chunk 73 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6869 Z= 0.234 Angle : 0.590 8.385 9426 Z= 0.297 Chirality : 0.044 0.163 1085 Planarity : 0.004 0.052 1097 Dihedral : 14.310 84.474 1207 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.35 % Favored : 93.39 % Rotamer: Outliers : 1.89 % Allowed : 18.63 % Favored : 79.48 % 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: -0.04 (0.31), residues: 756 helix: 1.98 (0.34), residues: 246 sheet: 0.14 (0.38), residues: 199 loop : -1.86 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 358 HIS 0.003 0.001 HIS A 903 PHE 0.028 0.002 PHE A 603 TYR 0.028 0.001 TYR A 679 ARG 0.003 0.000 ARG A 384 *********************** 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 95 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.713 Fit side-chains REVERT: A 471 ILE cc_start: 0.6199 (OUTLIER) cc_final: 0.5823 (mt) REVERT: A 865 HIS cc_start: 0.5941 (OUTLIER) cc_final: 0.5606 (p90) outliers start: 13 outliers final: 10 residues processed: 90 average time/residue: 0.1999 time to fit residues: 24.2183 Evaluate side-chains 87 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 471 ILE Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 499 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 865 HIS 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 8 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 33 optimal weight: 0.0020 chunk 29 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS A 819 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6869 Z= 0.268 Angle : 0.611 10.540 9426 Z= 0.306 Chirality : 0.044 0.170 1085 Planarity : 0.004 0.048 1097 Dihedral : 14.210 83.715 1207 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.69 % Favored : 94.05 % Rotamer: Outliers : 1.75 % Allowed : 19.07 % 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 (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: -0.04 (0.31), residues: 756 helix: 1.99 (0.34), residues: 245 sheet: 0.14 (0.38), residues: 200 loop : -1.87 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 358 HIS 0.003 0.001 HIS A 903 PHE 0.026 0.002 PHE A 603 TYR 0.021 0.001 TYR A 679 ARG 0.002 0.000 ARG A 750 *********************** 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 88 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.887 Fit side-chains REVERT: A 471 ILE cc_start: 0.6325 (OUTLIER) cc_final: 0.5926 (mt) REVERT: A 483 MET cc_start: -0.0983 (ttp) cc_final: -0.1572 (ppp) outliers start: 12 outliers final: 10 residues processed: 83 average time/residue: 0.2108 time to fit residues: 23.3334 Evaluate side-chains 86 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 471 ILE Chi-restraints excluded: chain A residue 498 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 57 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 6869 Z= 0.162 Angle : 0.554 10.284 9426 Z= 0.280 Chirality : 0.042 0.168 1085 Planarity : 0.004 0.047 1097 Dihedral : 14.090 84.743 1207 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.16 % Favored : 94.58 % Rotamer: Outliers : 0.87 % Allowed : 20.23 % 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: 0.07 (0.31), residues: 756 helix: 2.05 (0.34), residues: 249 sheet: 0.19 (0.38), residues: 199 loop : -1.81 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 358 HIS 0.002 0.000 HIS A 877 PHE 0.024 0.002 PHE A 603 TYR 0.017 0.001 TYR A 679 ARG 0.003 0.000 ARG A 384 *********************** 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 88 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.701 Fit side-chains REVERT: A 471 ILE cc_start: 0.6272 (OUTLIER) cc_final: 0.5865 (mt) REVERT: A 483 MET cc_start: -0.0974 (ttp) cc_final: -0.1554 (ppp) outliers start: 6 outliers final: 4 residues processed: 87 average time/residue: 0.2249 time to fit residues: 25.9592 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 : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 471 ILE 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 29 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS A 352 GLN A 540 ASN A 819 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 6869 Z= 0.420 Angle : 0.671 10.597 9426 Z= 0.339 Chirality : 0.047 0.164 1085 Planarity : 0.005 0.046 1097 Dihedral : 14.163 85.043 1207 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.82 % Favored : 93.92 % Rotamer: Outliers : 2.18 % Allowed : 19.65 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.90 (0.34), residues: 245 sheet: 0.09 (0.37), residues: 199 loop : -2.00 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 358 HIS 0.005 0.001 HIS A 893 PHE 0.032 0.003 PHE A 341 TYR 0.023 0.002 TYR A 859 ARG 0.003 0.000 ARG A 812 *********************** 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 92 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.788 Fit side-chains REVERT: A 471 ILE cc_start: 0.6330 (OUTLIER) cc_final: 0.5897 (mt) REVERT: A 483 MET cc_start: -0.1011 (ttp) cc_final: -0.1589 (ppp) REVERT: A 632 MET cc_start: 0.8048 (ttt) cc_final: 0.7448 (ttt) outliers start: 15 outliers final: 11 residues processed: 87 average time/residue: 0.1900 time to fit residues: 22.6989 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 : 0.724 ------------------------------------------------------------------------------- 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 471 ILE Chi-restraints excluded: chain A residue 498 MET 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 69 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 chunk 16 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN A 540 ASN A 801 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6869 Z= 0.171 Angle : 0.573 10.457 9426 Z= 0.290 Chirality : 0.043 0.153 1085 Planarity : 0.004 0.046 1097 Dihedral : 14.014 84.699 1207 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.42 % Favored : 94.31 % Rotamer: Outliers : 0.73 % Allowed : 21.83 % 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: -0.02 (0.31), residues: 756 helix: 2.02 (0.34), residues: 248 sheet: 0.17 (0.38), residues: 199 loop : -1.92 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 358 HIS 0.003 0.001 HIS A 353 PHE 0.028 0.002 PHE A 603 TYR 0.017 0.001 TYR A 679 ARG 0.004 0.000 ARG A 384 ********************** 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 87 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.756 Fit side-chains REVERT: A 471 ILE cc_start: 0.6415 (OUTLIER) cc_final: 0.5977 (mt) REVERT: A 483 MET cc_start: -0.1036 (ttp) cc_final: -0.1605 (ppp) outliers start: 5 outliers final: 4 residues processed: 86 average time/residue: 0.1959 time to fit residues: 22.6405 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 : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 471 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 7.9990 chunk 25 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.188002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.121883 restraints weight = 7743.445| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.79 r_work: 0.3295 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6869 Z= 0.269 Angle : 0.608 10.333 9426 Z= 0.305 Chirality : 0.044 0.161 1085 Planarity : 0.004 0.045 1097 Dihedral : 14.025 82.390 1207 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.95 % Favored : 93.92 % 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 (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: -0.02 (0.31), residues: 756 helix: 2.02 (0.35), residues: 247 sheet: 0.13 (0.37), residues: 200 loop : -1.88 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 358 HIS 0.003 0.001 HIS A 892 PHE 0.026 0.002 PHE A 603 TYR 0.016 0.001 TYR A 859 ARG 0.002 0.000 ARG A 384 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1609.40 seconds wall clock time: 30 minutes 21.63 seconds (1821.63 seconds total)