Starting phenix.real_space_refine on Fri May 9 16:42:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fcj_50317/05_2025/9fcj_50317.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fcj_50317/05_2025/9fcj_50317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fcj_50317/05_2025/9fcj_50317.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fcj_50317/05_2025/9fcj_50317.map" model { file = "/net/cci-nas-00/data/ceres_data/9fcj_50317/05_2025/9fcj_50317.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fcj_50317/05_2025/9fcj_50317.cif" } resolution = 2.7 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= 0.000 sd= 0.026 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 14 5.16 5 C 2010 2.51 5 N 524 2.21 5 O 625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3174 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 607 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2508 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 299} Chain breaks: 6 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' ZN': 1, 'JDA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1676 SG CYS D 440 37.181 76.326 21.625 1.00 9.31 S ATOM 1699 SG CYS D 443 38.872 76.870 18.330 1.00 10.42 S ATOM 2074 SG CYS D 506 40.932 75.662 21.048 1.00 8.96 S ATOM 2097 SG CYS D 509 39.780 79.274 21.029 1.00 9.66 S Time building chain proxies: 3.13, per 1000 atoms: 0.99 Number of scatterers: 3174 At special positions: 0 Unit cell: (66.78, 90.1, 58.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 14 16.00 O 625 8.00 N 524 7.00 C 2010 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: 0.82 Conformation dependent library (CDL) restraints added in 398.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 443 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 509 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 440 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 506 " Number of angles added : 6 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 7 sheets defined 45.0% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'C' and resid 22 through 35 removed outlier: 3.595A pdb=" N LYS C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'D' and resid 81 through 88 removed outlier: 4.142A pdb=" N ASN D 85 " --> pdb=" O GLY D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 101 removed outlier: 3.741A pdb=" N ILE D 95 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE D 101 " --> pdb=" O GLN D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 120 Processing helix chain 'D' and resid 144 through 166 Processing helix chain 'D' and resid 166 through 177 removed outlier: 3.787A pdb=" N ASP D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 189 removed outlier: 3.962A pdb=" N LEU D 181 " --> pdb=" O GLN D 177 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 220 Processing helix chain 'D' and resid 424 through 431 Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 499 through 503 removed outlier: 3.685A pdb=" N LYS D 503 " --> pdb=" O GLY D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 568 Processing helix chain 'D' and resid 759 through 767 Processing helix chain 'D' and resid 768 through 772 Processing sheet with id=AA1, first strand: chain 'C' and resid 12 through 17 removed outlier: 9.096A pdb=" N LEU C 67 " --> pdb=" O GLN C 2 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE C 4 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU C 69 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LYS C 6 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 74 through 75 Processing sheet with id=AA3, first strand: chain 'D' and resid 446 through 453 removed outlier: 6.395A pdb=" N GLN D 433 " --> pdb=" O ASP D 522 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 456 through 459 removed outlier: 6.118A pdb=" N ILE D 456 " --> pdb=" O HIS D 531 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS D 533 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL D 458 " --> pdb=" O LYS D 533 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR D 778 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL D 582 " --> pdb=" O TYR D 778 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU D 780 " --> pdb=" O ALA D 580 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA D 580 " --> pdb=" O LEU D 780 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR D 782 " --> pdb=" O LEU D 578 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU D 578 " --> pdb=" O TYR D 782 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS D 784 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR D 576 " --> pdb=" O LYS D 784 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 456 through 459 removed outlier: 6.118A pdb=" N ILE D 456 " --> pdb=" O HIS D 531 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS D 533 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL D 458 " --> pdb=" O LYS D 533 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR D 778 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL D 582 " --> pdb=" O TYR D 778 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU D 780 " --> pdb=" O ALA D 580 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA D 580 " --> pdb=" O LEU D 780 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR D 782 " --> pdb=" O LEU D 578 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU D 578 " --> pdb=" O TYR D 782 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS D 784 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR D 576 " --> pdb=" O LYS D 784 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE D 579 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA D 596 " --> pdb=" O PHE D 750 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 504 through 506 Processing sheet with id=AA7, first strand: chain 'D' and resid 535 through 536 181 hydrogen bonds defined for protein. 459 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1006 1.34 - 1.46: 595 1.46 - 1.58: 1577 1.58 - 1.69: 0 1.69 - 1.81: 19 Bond restraints: 3197 Sorted by residual: bond pdb=" C12 JDA D1001 " pdb=" C13 JDA D1001 " ideal model delta sigma weight residual 1.371 1.352 0.019 2.00e-02 2.50e+03 9.38e-01 bond pdb=" C16 JDA D1001 " pdb=" C17 JDA D1001 " ideal model delta sigma weight residual 1.392 1.375 0.017 2.00e-02 2.50e+03 7.31e-01 bond pdb=" CB GLU C 51 " pdb=" CG GLU C 51 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.65e-01 bond pdb=" CG GLU C 51 " pdb=" CD GLU C 51 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 6.07e-01 bond pdb=" C PRO D 777 " pdb=" N TYR D 778 " ideal model delta sigma weight residual 1.329 1.315 0.014 1.79e-02 3.12e+03 6.00e-01 ... (remaining 3192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 4241 1.65 - 3.31: 63 3.31 - 4.96: 5 4.96 - 6.62: 1 6.62 - 8.27: 2 Bond angle restraints: 4312 Sorted by residual: angle pdb=" CB MET D 524 " pdb=" CG MET D 524 " pdb=" SD MET D 524 " ideal model delta sigma weight residual 112.70 120.97 -8.27 3.00e+00 1.11e-01 7.60e+00 angle pdb=" C VAL C 17 " pdb=" N GLU C 18 " pdb=" CA GLU C 18 " ideal model delta sigma weight residual 122.15 129.70 -7.55 3.47e+00 8.31e-02 4.73e+00 angle pdb=" CB GLU C 51 " pdb=" CG GLU C 51 " pdb=" CD GLU C 51 " ideal model delta sigma weight residual 112.60 115.97 -3.37 1.70e+00 3.46e-01 3.92e+00 angle pdb=" CA LYS D 533 " pdb=" C LYS D 533 " pdb=" N CYS D 534 " ideal model delta sigma weight residual 114.76 116.96 -2.20 1.14e+00 7.69e-01 3.71e+00 angle pdb=" CA LYS D 533 " pdb=" C LYS D 533 " pdb=" O LYS D 533 " ideal model delta sigma weight residual 122.64 120.43 2.21 1.25e+00 6.40e-01 3.12e+00 ... (remaining 4307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 1709 17.37 - 34.73: 173 34.73 - 52.10: 52 52.10 - 69.46: 12 69.46 - 86.83: 5 Dihedral angle restraints: 1951 sinusoidal: 818 harmonic: 1133 Sorted by residual: dihedral pdb=" CG ARG D 517 " pdb=" CD ARG D 517 " pdb=" NE ARG D 517 " pdb=" CZ ARG D 517 " ideal model delta sinusoidal sigma weight residual -180.00 -136.99 -43.01 2 1.50e+01 4.44e-03 9.93e+00 dihedral pdb=" CB GLU D 760 " pdb=" CG GLU D 760 " pdb=" CD GLU D 760 " pdb=" OE1 GLU D 760 " ideal model delta sinusoidal sigma weight residual 0.00 -85.95 85.95 1 3.00e+01 1.11e-03 9.91e+00 dihedral pdb=" CA ASP D 463 " pdb=" CB ASP D 463 " pdb=" CG ASP D 463 " pdb=" OD1 ASP D 463 " ideal model delta sinusoidal sigma weight residual -30.00 -83.61 53.61 1 2.00e+01 2.50e-03 9.76e+00 ... (remaining 1948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 317 0.026 - 0.052: 111 0.052 - 0.078: 42 0.078 - 0.104: 19 0.104 - 0.130: 9 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA ILE C 36 " pdb=" N ILE C 36 " pdb=" C ILE C 36 " pdb=" CB ILE C 36 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL D 755 " pdb=" N VAL D 755 " pdb=" C VAL D 755 " pdb=" CB VAL D 755 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA ILE D 552 " pdb=" N ILE D 552 " pdb=" C ILE D 552 " pdb=" CB ILE D 552 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 495 not shown) Planarity restraints: 541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 JDA D1001 " 0.017 2.00e-02 2.50e+03 2.34e-02 1.09e+01 pdb=" C11 JDA D1001 " 0.015 2.00e-02 2.50e+03 pdb=" C5 JDA D1001 " -0.038 2.00e-02 2.50e+03 pdb=" C6 JDA D1001 " 0.007 2.00e-02 2.50e+03 pdb=" C7 JDA D1001 " 0.015 2.00e-02 2.50e+03 pdb=" C8 JDA D1001 " 0.017 2.00e-02 2.50e+03 pdb=" C9 JDA D1001 " 0.010 2.00e-02 2.50e+03 pdb=" N3 JDA D1001 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N JDA D1001 " -0.017 2.00e-02 2.50e+03 1.82e-02 7.44e+00 pdb=" C JDA D1001 " 0.033 2.00e-02 2.50e+03 pdb=" C1 JDA D1001 " -0.006 2.00e-02 2.50e+03 pdb=" C14 JDA D1001 " 0.012 2.00e-02 2.50e+03 pdb=" C2 JDA D1001 " -0.020 2.00e-02 2.50e+03 pdb=" C3 JDA D1001 " 0.008 2.00e-02 2.50e+03 pdb=" C4 JDA D1001 " 0.001 2.00e-02 2.50e+03 pdb=" N1 JDA D1001 " 0.015 2.00e-02 2.50e+03 pdb=" N2 JDA D1001 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 163 " 0.009 2.00e-02 2.50e+03 1.02e-02 1.83e+00 pdb=" CG PHE D 163 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE D 163 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE D 163 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 163 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 163 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 163 " 0.000 2.00e-02 2.50e+03 ... (remaining 538 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 361 2.75 - 3.29: 2854 3.29 - 3.83: 5172 3.83 - 4.36: 6786 4.36 - 4.90: 11174 Nonbonded interactions: 26347 Sorted by model distance: nonbonded pdb=" O LEU C 73 " pdb=" OH TYR D 594 " model vdw 2.213 3.040 nonbonded pdb=" OE1 GLU D 202 " pdb=" O HOH D1101 " model vdw 2.233 3.040 nonbonded pdb=" O CYS D 102 " pdb=" O HOH D1102 " model vdw 2.234 3.040 nonbonded pdb=" O HOH D1109 " pdb=" O HOH D1112 " model vdw 2.276 3.040 nonbonded pdb=" NH1 ARG D 517 " pdb=" O HOH D1103 " model vdw 2.352 3.120 ... (remaining 26342 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.880 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 : 0.003 0.038 3201 Z= 0.140 Angle : 0.571 8.272 4318 Z= 0.292 Chirality : 0.036 0.130 498 Planarity : 0.004 0.031 541 Dihedral : 16.442 86.830 1211 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.56 % Allowed : 10.89 % Favored : 88.55 % 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: 0.06 (0.41), residues: 373 helix: 0.10 (0.42), residues: 140 sheet: 0.43 (0.46), residues: 102 loop : -0.09 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 487 HIS 0.002 0.001 HIS C 68 PHE 0.024 0.002 PHE D 163 TYR 0.011 0.001 TYR D 504 ARG 0.005 0.001 ARG D 186 Details of bonding type rmsd hydrogen bonds : bond 0.22020 ( 173) hydrogen bonds : angle 7.44694 ( 459) metal coordination : bond 0.02193 ( 4) metal coordination : angle 4.39203 ( 6) covalent geometry : bond 0.00301 ( 3197) covalent geometry : angle 0.54746 ( 4312) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.385 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 68 average time/residue: 1.3584 time to fit residues: 94.7070 Evaluate side-chains 64 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 455 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.131452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.104035 restraints weight = 3480.221| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.84 r_work: 0.2968 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3201 Z= 0.178 Angle : 0.561 5.965 4318 Z= 0.286 Chirality : 0.040 0.125 498 Planarity : 0.004 0.031 541 Dihedral : 5.339 41.254 426 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.96 % Allowed : 13.13 % Favored : 84.92 % 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: 0.79 (0.42), residues: 373 helix: 1.06 (0.42), residues: 143 sheet: 0.35 (0.45), residues: 104 loop : 0.28 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 487 HIS 0.003 0.001 HIS D 584 PHE 0.012 0.002 PHE D 505 TYR 0.010 0.001 TYR D 782 ARG 0.007 0.001 ARG D 186 Details of bonding type rmsd hydrogen bonds : bond 0.04583 ( 173) hydrogen bonds : angle 4.95494 ( 459) metal coordination : bond 0.00373 ( 4) metal coordination : angle 2.31408 ( 6) covalent geometry : bond 0.00410 ( 3197) covalent geometry : angle 0.55512 ( 4312) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.417 Fit side-chains REVERT: D 110 LYS cc_start: 0.7201 (tttm) cc_final: 0.6866 (ttmm) REVERT: D 565 GLU cc_start: 0.7962 (tt0) cc_final: 0.7633 (pt0) outliers start: 7 outliers final: 2 residues processed: 66 average time/residue: 1.3610 time to fit residues: 92.1537 Evaluate side-chains 61 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN D 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.130377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.103315 restraints weight = 3397.393| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.81 r_work: 0.2959 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3201 Z= 0.202 Angle : 0.555 5.733 4318 Z= 0.279 Chirality : 0.040 0.135 498 Planarity : 0.004 0.028 541 Dihedral : 5.313 42.507 424 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.40 % Allowed : 15.64 % Favored : 82.96 % 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: 0.85 (0.42), residues: 373 helix: 1.29 (0.42), residues: 143 sheet: 0.26 (0.46), residues: 104 loop : 0.18 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 487 HIS 0.004 0.001 HIS D 584 PHE 0.011 0.002 PHE D 505 TYR 0.012 0.002 TYR D 504 ARG 0.005 0.001 ARG D 186 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 173) hydrogen bonds : angle 4.69484 ( 459) metal coordination : bond 0.00411 ( 4) metal coordination : angle 2.09266 ( 6) covalent geometry : bond 0.00476 ( 3197) covalent geometry : angle 0.55029 ( 4312) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.385 Fit side-chains REVERT: D 565 GLU cc_start: 0.7929 (tt0) cc_final: 0.7630 (pt0) outliers start: 5 outliers final: 4 residues processed: 65 average time/residue: 1.2942 time to fit residues: 86.4766 Evaluate side-chains 64 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 770 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.129864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.102474 restraints weight = 3460.346| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.86 r_work: 0.2957 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3201 Z= 0.202 Angle : 0.561 7.342 4318 Z= 0.279 Chirality : 0.040 0.142 498 Planarity : 0.004 0.035 541 Dihedral : 5.342 42.695 424 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.51 % Allowed : 15.64 % Favored : 81.84 % 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: 0.82 (0.42), residues: 373 helix: 1.34 (0.42), residues: 143 sheet: 0.16 (0.46), residues: 104 loop : 0.16 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 487 HIS 0.004 0.001 HIS D 584 PHE 0.011 0.002 PHE D 750 TYR 0.011 0.002 TYR D 504 ARG 0.008 0.001 ARG D 186 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 173) hydrogen bonds : angle 4.59995 ( 459) metal coordination : bond 0.00392 ( 4) metal coordination : angle 2.04151 ( 6) covalent geometry : bond 0.00475 ( 3197) covalent geometry : angle 0.55637 ( 4312) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.395 Fit side-chains REVERT: D 565 GLU cc_start: 0.8008 (tt0) cc_final: 0.7751 (pt0) REVERT: D 749 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8706 (mt) outliers start: 9 outliers final: 6 residues processed: 67 average time/residue: 1.2328 time to fit residues: 84.9613 Evaluate side-chains 65 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 770 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 0.0270 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.133037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.106001 restraints weight = 3420.747| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.84 r_work: 0.3014 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3201 Z= 0.103 Angle : 0.487 7.970 4318 Z= 0.241 Chirality : 0.037 0.132 498 Planarity : 0.003 0.029 541 Dihedral : 4.959 41.338 424 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.35 % Allowed : 14.80 % Favored : 81.84 % 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: 1.23 (0.43), residues: 373 helix: 1.80 (0.42), residues: 143 sheet: 0.26 (0.47), residues: 104 loop : 0.34 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 747 HIS 0.002 0.001 HIS D 584 PHE 0.008 0.001 PHE D 453 TYR 0.008 0.001 TYR D 504 ARG 0.008 0.001 ARG D 186 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 173) hydrogen bonds : angle 4.25849 ( 459) metal coordination : bond 0.00318 ( 4) metal coordination : angle 1.92487 ( 6) covalent geometry : bond 0.00232 ( 3197) covalent geometry : angle 0.48219 ( 4312) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.405 Fit side-chains REVERT: D 213 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6464 (pt0) REVERT: D 433 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8160 (mt0) REVERT: D 455 ASP cc_start: 0.8120 (p0) cc_final: 0.7785 (p0) REVERT: D 483 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8191 (mmpt) REVERT: D 749 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8651 (mt) REVERT: D 764 LEU cc_start: 0.8164 (mm) cc_final: 0.7964 (mp) outliers start: 12 outliers final: 5 residues processed: 64 average time/residue: 1.0633 time to fit residues: 70.3609 Evaluate side-chains 63 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 433 GLN Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 770 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.131698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.104406 restraints weight = 3490.932| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.87 r_work: 0.2979 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3201 Z= 0.142 Angle : 0.548 13.623 4318 Z= 0.262 Chirality : 0.038 0.132 498 Planarity : 0.003 0.025 541 Dihedral : 5.046 41.851 424 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.35 % Allowed : 15.92 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.43), residues: 373 helix: 1.85 (0.42), residues: 143 sheet: 0.27 (0.48), residues: 104 loop : 0.32 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 487 HIS 0.003 0.001 HIS D 584 PHE 0.008 0.001 PHE D 750 TYR 0.011 0.001 TYR D 576 ARG 0.005 0.001 ARG D 186 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 173) hydrogen bonds : angle 4.26985 ( 459) metal coordination : bond 0.00311 ( 4) metal coordination : angle 1.70435 ( 6) covalent geometry : bond 0.00333 ( 3197) covalent geometry : angle 0.54467 ( 4312) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.363 Fit side-chains REVERT: D 84 ASN cc_start: 0.7022 (OUTLIER) cc_final: 0.6675 (p0) REVERT: D 213 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6453 (pt0) REVERT: D 433 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8234 (mt0) REVERT: D 455 ASP cc_start: 0.8084 (p0) cc_final: 0.7737 (p0) REVERT: D 483 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8177 (mmpt) REVERT: D 749 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8654 (mt) REVERT: D 764 LEU cc_start: 0.8126 (mm) cc_final: 0.7918 (mp) outliers start: 12 outliers final: 6 residues processed: 63 average time/residue: 1.0636 time to fit residues: 69.1775 Evaluate side-chains 65 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 433 GLN Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 770 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.130113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.102620 restraints weight = 3486.658| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.87 r_work: 0.2991 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3201 Z= 0.215 Angle : 0.582 9.442 4318 Z= 0.286 Chirality : 0.040 0.134 498 Planarity : 0.004 0.027 541 Dihedral : 5.311 42.602 424 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.35 % Allowed : 15.92 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.43), residues: 373 helix: 1.57 (0.42), residues: 143 sheet: 0.16 (0.48), residues: 104 loop : 0.25 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 487 HIS 0.004 0.001 HIS D 584 PHE 0.012 0.002 PHE D 750 TYR 0.013 0.002 TYR D 504 ARG 0.004 0.001 ARG D 186 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 173) hydrogen bonds : angle 4.44569 ( 459) metal coordination : bond 0.00364 ( 4) metal coordination : angle 1.83403 ( 6) covalent geometry : bond 0.00511 ( 3197) covalent geometry : angle 0.57882 ( 4312) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.421 Fit side-chains REVERT: D 110 LYS cc_start: 0.7168 (tttm) cc_final: 0.6865 (ttmm) REVERT: D 213 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6480 (pt0) REVERT: D 433 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8278 (mt0) REVERT: D 483 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8177 (mmpt) REVERT: D 749 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8641 (mt) REVERT: D 764 LEU cc_start: 0.8170 (mm) cc_final: 0.7969 (mp) outliers start: 12 outliers final: 6 residues processed: 72 average time/residue: 1.2207 time to fit residues: 90.3886 Evaluate side-chains 72 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 433 GLN Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 770 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 37 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.131896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.104577 restraints weight = 3440.785| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.86 r_work: 0.3029 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3201 Z= 0.122 Angle : 0.535 12.547 4318 Z= 0.258 Chirality : 0.037 0.129 498 Planarity : 0.003 0.027 541 Dihedral : 5.053 41.439 424 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.07 % Allowed : 16.20 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.43), residues: 373 helix: 1.87 (0.42), residues: 142 sheet: 0.15 (0.49), residues: 104 loop : 0.38 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 487 HIS 0.003 0.001 HIS D 584 PHE 0.008 0.001 PHE D 453 TYR 0.010 0.001 TYR D 504 ARG 0.006 0.001 ARG D 186 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 173) hydrogen bonds : angle 4.22111 ( 459) metal coordination : bond 0.00290 ( 4) metal coordination : angle 1.69624 ( 6) covalent geometry : bond 0.00288 ( 3197) covalent geometry : angle 0.53135 ( 4312) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.409 Fit side-chains REVERT: D 110 LYS cc_start: 0.7110 (tttm) cc_final: 0.6820 (ttmm) REVERT: D 213 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6449 (pt0) REVERT: D 433 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8227 (mt0) REVERT: D 483 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8175 (mmpt) REVERT: D 749 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8657 (mt) outliers start: 11 outliers final: 5 residues processed: 67 average time/residue: 1.1838 time to fit residues: 81.6144 Evaluate side-chains 66 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 433 GLN Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 770 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 0.0030 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.132332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.105054 restraints weight = 3417.928| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.85 r_work: 0.2991 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3201 Z= 0.117 Angle : 0.525 11.565 4318 Z= 0.253 Chirality : 0.037 0.130 498 Planarity : 0.003 0.027 541 Dihedral : 4.936 41.322 424 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.23 % Allowed : 16.76 % Favored : 81.01 % 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: 1.39 (0.43), residues: 373 helix: 2.05 (0.42), residues: 142 sheet: 0.22 (0.49), residues: 104 loop : 0.40 (0.58), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 487 HIS 0.003 0.001 HIS D 584 PHE 0.007 0.001 PHE D 453 TYR 0.009 0.001 TYR D 504 ARG 0.006 0.001 ARG D 186 Details of bonding type rmsd hydrogen bonds : bond 0.03014 ( 173) hydrogen bonds : angle 4.13560 ( 459) metal coordination : bond 0.00263 ( 4) metal coordination : angle 1.48791 ( 6) covalent geometry : bond 0.00274 ( 3197) covalent geometry : angle 0.52237 ( 4312) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.417 Fit side-chains REVERT: D 110 LYS cc_start: 0.7124 (tttm) cc_final: 0.6819 (ttmm) REVERT: D 213 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6858 (tt0) REVERT: D 433 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8234 (mt0) REVERT: D 455 ASP cc_start: 0.8024 (p0) cc_final: 0.7702 (p0) REVERT: D 483 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8139 (mmpt) REVERT: D 749 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8639 (mt) outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 1.1346 time to fit residues: 76.0201 Evaluate side-chains 65 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 433 GLN Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 0.0980 chunk 30 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.133100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.105710 restraints weight = 3410.772| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.85 r_work: 0.3000 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3201 Z= 0.109 Angle : 0.527 12.893 4318 Z= 0.252 Chirality : 0.036 0.130 498 Planarity : 0.003 0.028 541 Dihedral : 4.851 40.923 424 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.96 % Allowed : 17.04 % Favored : 81.01 % 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: 1.52 (0.44), residues: 373 helix: 2.18 (0.42), residues: 142 sheet: 0.27 (0.49), residues: 104 loop : 0.46 (0.59), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 747 HIS 0.002 0.001 HIS D 584 PHE 0.008 0.001 PHE D 579 TYR 0.009 0.001 TYR D 504 ARG 0.006 0.000 ARG D 186 Details of bonding type rmsd hydrogen bonds : bond 0.02873 ( 173) hydrogen bonds : angle 4.06418 ( 459) metal coordination : bond 0.00259 ( 4) metal coordination : angle 1.53873 ( 6) covalent geometry : bond 0.00256 ( 3197) covalent geometry : angle 0.52392 ( 4312) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.427 Fit side-chains REVERT: D 110 LYS cc_start: 0.7138 (tttm) cc_final: 0.6815 (ttmm) REVERT: D 213 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6845 (tt0) REVERT: D 433 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8207 (mt0) REVERT: D 455 ASP cc_start: 0.7911 (p0) cc_final: 0.7587 (p0) REVERT: D 483 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8133 (mmpt) REVERT: D 572 THR cc_start: 0.7759 (p) cc_final: 0.7450 (t) REVERT: D 749 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8619 (mt) outliers start: 7 outliers final: 4 residues processed: 64 average time/residue: 1.2182 time to fit residues: 80.3116 Evaluate side-chains 65 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 433 GLN Chi-restraints excluded: chain D residue 483 LYS Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 34 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.104766 restraints weight = 3433.737| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.86 r_work: 0.3030 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3201 Z= 0.132 Angle : 0.557 14.288 4318 Z= 0.265 Chirality : 0.037 0.130 498 Planarity : 0.003 0.029 541 Dihedral : 4.947 41.296 424 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.23 % Allowed : 17.32 % Favored : 80.45 % 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: 1.49 (0.44), residues: 373 helix: 2.13 (0.42), residues: 142 sheet: 0.26 (0.50), residues: 104 loop : 0.48 (0.59), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 487 HIS 0.003 0.001 HIS D 584 PHE 0.007 0.001 PHE D 750 TYR 0.010 0.001 TYR D 504 ARG 0.006 0.001 ARG D 186 Details of bonding type rmsd hydrogen bonds : bond 0.03072 ( 173) hydrogen bonds : angle 4.10328 ( 459) metal coordination : bond 0.00276 ( 4) metal coordination : angle 1.50859 ( 6) covalent geometry : bond 0.00315 ( 3197) covalent geometry : angle 0.55409 ( 4312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2817.69 seconds wall clock time: 49 minutes 21.07 seconds (2961.07 seconds total)