Starting phenix.real_space_refine on Fri Aug 22 17:00:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9y_45376/08_2025/9c9y_45376_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9y_45376/08_2025/9c9y_45376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c9y_45376/08_2025/9c9y_45376_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9y_45376/08_2025/9c9y_45376_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c9y_45376/08_2025/9c9y_45376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9y_45376/08_2025/9c9y_45376.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 Mn 2 7.51 5 P 8 5.49 5 S 39 5.16 5 C 3908 2.51 5 N 1077 2.21 5 O 1191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6225 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4840 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 30, 'TRANS': 581} Chain: "B" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1219 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "C" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 164 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.84, per 1000 atoms: 0.30 Number of scatterers: 6225 At special positions: 0 Unit cell: (69.72, 87.15, 136.12, 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) Mn 2 24.99 S 39 16.00 P 8 15.00 O 1191 8.00 N 1077 7.00 C 3908 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: 0.42 Conformation dependent library (CDL) restraints added in 333.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1442 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 7 sheets defined 40.9% alpha, 20.8% beta 0 base pairs and 3 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 77 through 82 removed outlier: 3.622A pdb=" N PHE A 82 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 107 Processing helix chain 'A' and resid 119 through 134 removed outlier: 4.160A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 166 Processing helix chain 'A' and resid 171 through 200 removed outlier: 3.743A pdb=" N SER A 177 " --> pdb=" O ASN A 173 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 194 " --> pdb=" O CYS A 190 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.632A pdb=" N CYS A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 Processing helix chain 'A' and resid 302 through 314 Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 349 through 357 removed outlier: 3.832A pdb=" N GLN A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.687A pdb=" N TYR A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 456 through 460 Processing helix chain 'A' and resid 495 through 507 removed outlier: 3.725A pdb=" N LYS A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 538 through 552 removed outlier: 3.750A pdb=" N LYS A 550 " --> pdb=" O HIS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 574 removed outlier: 4.193A pdb=" N SER A 562 " --> pdb=" O PRO A 558 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 570 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE A 571 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 599 removed outlier: 3.954A pdb=" N HIS A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 589 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP A 598 " --> pdb=" O HIS A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 606 through 610 removed outlier: 3.895A pdb=" N VAL A 609 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 removed outlier: 3.664A pdb=" N ALA B 7 " --> pdb=" O GLN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 25 Processing helix chain 'B' and resid 32 through 41 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 5.780A pdb=" N SER A 37 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER A 56 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR A 3 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N VAL A 113 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU A 5 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N TRP A 115 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL A 7 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE A 112 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 253 through 256 removed outlier: 7.037A pdb=" N ARG A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL A 242 " --> pdb=" O MET A 483 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N MET A 483 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLN A 244 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL A 481 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS A 246 " --> pdb=" O GLY A 479 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N ASP A 250 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 13.734A pdb=" N ALA A 475 " --> pdb=" O ASP A 250 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER A 432 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR A 288 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR A 430 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS A 425 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 253 through 256 removed outlier: 7.037A pdb=" N ARG A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL A 242 " --> pdb=" O MET A 483 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N MET A 483 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLN A 244 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL A 481 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS A 246 " --> pdb=" O GLY A 479 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N ASP A 250 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 13.734A pdb=" N ALA A 475 " --> pdb=" O ASP A 250 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER A 432 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR A 288 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR A 430 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS A 424 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 291 " --> pdb=" O GLN A 428 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 527 through 530 removed outlier: 3.679A pdb=" N ARG A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 65 through 66 Processing sheet with id=AA7, first strand: chain 'B' and resid 139 through 141 removed outlier: 3.884A pdb=" N ILE B 104 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ARG B 96 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE B 76 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLN B 98 " --> pdb=" O GLN B 74 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 786 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 3 stacking parallelities Total time for adding SS restraints: 0.81 Time building geometry restraints manager: 0.56 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: 1997 1.34 - 1.45: 883 1.45 - 1.57: 3413 1.57 - 1.69: 13 1.69 - 1.81: 61 Bond restraints: 6367 Sorted by residual: bond pdb=" O3' DT C 1 " pdb=" P DA C 2 " ideal model delta sigma weight residual 1.607 1.556 0.051 1.50e-02 4.44e+03 1.15e+01 bond pdb=" O3' DA C 2 " pdb=" P DA C 3 " ideal model delta sigma weight residual 1.607 1.559 0.048 1.50e-02 4.44e+03 1.03e+01 bond pdb=" O3' DC C 0 " pdb=" P DT C 1 " ideal model delta sigma weight residual 1.607 1.572 0.035 1.50e-02 4.44e+03 5.34e+00 bond pdb=" C TRP A 73 " pdb=" N ASP A 74 " ideal model delta sigma weight residual 1.332 1.303 0.029 1.41e-02 5.03e+03 4.32e+00 bond pdb=" CG LEU A 114 " pdb=" CD1 LEU A 114 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.90e+00 ... (remaining 6362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 8362 1.58 - 3.15: 229 3.15 - 4.73: 34 4.73 - 6.31: 18 6.31 - 7.89: 4 Bond angle restraints: 8647 Sorted by residual: angle pdb=" C4' DA C 2 " pdb=" C3' DA C 2 " pdb=" O3' DA C 2 " ideal model delta sigma weight residual 110.00 104.30 5.70 1.50e+00 4.44e-01 1.45e+01 angle pdb=" C3' DT C 6 " pdb=" C2' DT C 6 " pdb=" C1' DT C 6 " ideal model delta sigma weight residual 101.60 105.56 -3.96 1.50e+00 4.44e-01 6.97e+00 angle pdb=" CB MET A 272 " pdb=" CG MET A 272 " pdb=" SD MET A 272 " ideal model delta sigma weight residual 112.70 120.59 -7.89 3.00e+00 1.11e-01 6.91e+00 angle pdb=" C ALA A 553 " pdb=" N GLU A 554 " pdb=" CA GLU A 554 " ideal model delta sigma weight residual 121.58 116.62 4.96 1.95e+00 2.63e-01 6.48e+00 angle pdb=" N SER B 27 " pdb=" CA SER B 27 " pdb=" C SER B 27 " ideal model delta sigma weight residual 109.81 115.40 -5.59 2.21e+00 2.05e-01 6.40e+00 ... (remaining 8642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.02: 3645 29.02 - 58.04: 196 58.04 - 87.06: 14 87.06 - 116.08: 0 116.08 - 145.10: 1 Dihedral angle restraints: 3856 sinusoidal: 1622 harmonic: 2234 Sorted by residual: dihedral pdb=" CD ARG A 149 " pdb=" NE ARG A 149 " pdb=" CZ ARG A 149 " pdb=" NH1 ARG A 149 " ideal model delta sinusoidal sigma weight residual 0.00 71.03 -71.03 1 1.00e+01 1.00e-02 6.48e+01 dihedral pdb=" CG ARG B 77 " pdb=" CD ARG B 77 " pdb=" NE ARG B 77 " pdb=" CZ ARG B 77 " ideal model delta sinusoidal sigma weight residual -90.00 -32.53 -57.47 2 1.50e+01 4.44e-03 1.52e+01 dihedral pdb=" C4' DA C -1 " pdb=" C3' DA C -1 " pdb=" O3' DA C -1 " pdb=" P DC C 0 " ideal model delta sinusoidal sigma weight residual 220.00 74.90 145.10 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 3853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 572 0.033 - 0.066: 274 0.066 - 0.100: 84 0.100 - 0.133: 37 0.133 - 0.166: 3 Chirality restraints: 970 Sorted by residual: chirality pdb=" CB ILE A 155 " pdb=" CA ILE A 155 " pdb=" CG1 ILE A 155 " pdb=" CG2 ILE A 155 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA ILE A 435 " pdb=" N ILE A 435 " pdb=" C ILE A 435 " pdb=" CB ILE A 435 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA THR A 219 " pdb=" N THR A 219 " pdb=" C THR A 219 " pdb=" CB THR A 219 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 967 not shown) Planarity restraints: 1090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 149 " 1.040 9.50e-02 1.11e+02 4.66e-01 1.31e+02 pdb=" NE ARG A 149 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG A 149 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 149 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 149 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 27 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO B 28 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 28 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 28 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 476 " -0.037 5.00e-02 4.00e+02 5.59e-02 5.01e+00 pdb=" N PRO A 477 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 477 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 477 " -0.031 5.00e-02 4.00e+02 ... (remaining 1087 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 51 2.61 - 3.18: 5211 3.18 - 3.76: 8887 3.76 - 4.33: 11637 4.33 - 4.90: 19671 Nonbonded interactions: 45457 Sorted by model distance: nonbonded pdb=" OD2 ASP A 511 " pdb="MN MN A 702 " model vdw 2.041 2.320 nonbonded pdb=" OP1 DA C 5 " pdb="MN MN A 701 " model vdw 2.114 2.320 nonbonded pdb=" OD2 ASP A 117 " pdb="MN MN A 701 " model vdw 2.120 2.320 nonbonded pdb=" OE2 GLU A 340 " pdb="MN MN A 702 " model vdw 2.158 2.320 nonbonded pdb=" O ALA A 18 " pdb=" OG SER A 22 " model vdw 2.185 3.040 ... (remaining 45452 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: 3.890 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.390 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 : 0.005 0.056 6367 Z= 0.240 Angle : 0.664 7.886 8647 Z= 0.343 Chirality : 0.044 0.166 970 Planarity : 0.015 0.466 1090 Dihedral : 16.017 145.098 2414 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.98 % Favored : 93.89 % Rotamer: Outliers : 0.15 % Allowed : 0.60 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.31), residues: 769 helix: 1.05 (0.31), residues: 296 sheet: 0.25 (0.44), residues: 157 loop : -1.14 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 369 TYR 0.011 0.001 TYR A 549 PHE 0.014 0.002 PHE A 200 TRP 0.008 0.001 TRP A 73 HIS 0.003 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00537 ( 6367) covalent geometry : angle 0.66422 ( 8647) hydrogen bonds : bond 0.09483 ( 266) hydrogen bonds : angle 4.94655 ( 786) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.231 Fit side-chains REVERT: A 19 LYS cc_start: 0.8434 (tttp) cc_final: 0.8115 (tttp) REVERT: A 109 CYS cc_start: 0.7564 (m) cc_final: 0.7163 (m) REVERT: A 119 ASP cc_start: 0.6978 (p0) cc_final: 0.6753 (p0) REVERT: A 128 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6850 (tm-30) REVERT: A 226 VAL cc_start: 0.7580 (m) cc_final: 0.7362 (t) REVERT: A 246 LYS cc_start: 0.8562 (ptpt) cc_final: 0.8300 (ptpt) REVERT: A 282 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7117 (mm-30) REVERT: A 393 MET cc_start: 0.8285 (mtp) cc_final: 0.7919 (mtp) REVERT: A 511 ASP cc_start: 0.6125 (p0) cc_final: 0.5916 (p0) REVERT: A 566 LYS cc_start: 0.8167 (ttpp) cc_final: 0.7929 (ttpt) REVERT: B 32 ASN cc_start: 0.7825 (t0) cc_final: 0.7175 (t0) REVERT: B 95 LEU cc_start: 0.8416 (mm) cc_final: 0.7996 (mp) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.0971 time to fit residues: 27.5585 Evaluate side-chains 209 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.0770 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.112036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.099237 restraints weight = 9893.251| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.66 r_work: 0.3117 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6367 Z= 0.183 Angle : 0.616 8.370 8647 Z= 0.309 Chirality : 0.043 0.180 970 Planarity : 0.004 0.047 1090 Dihedral : 10.654 141.113 926 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.20 % Allowed : 13.92 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.31), residues: 769 helix: 1.14 (0.31), residues: 296 sheet: 0.34 (0.45), residues: 151 loop : -1.18 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 77 TYR 0.011 0.001 TYR A 329 PHE 0.014 0.001 PHE A 433 TRP 0.010 0.001 TRP A 406 HIS 0.006 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 6367) covalent geometry : angle 0.61635 ( 8647) hydrogen bonds : bond 0.04977 ( 266) hydrogen bonds : angle 4.57179 ( 786) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 223 time to evaluate : 0.251 Fit side-chains REVERT: A 65 ASP cc_start: 0.7672 (t0) cc_final: 0.7471 (t0) REVERT: A 109 CYS cc_start: 0.7907 (m) cc_final: 0.7497 (m) REVERT: A 128 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7063 (tm-30) REVERT: A 226 VAL cc_start: 0.7892 (m) cc_final: 0.7632 (t) REVERT: A 246 LYS cc_start: 0.8597 (ptpt) cc_final: 0.8331 (ptpt) REVERT: A 272 MET cc_start: 0.8110 (tmm) cc_final: 0.7826 (tmm) REVERT: A 282 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7395 (mm-30) REVERT: A 357 GLN cc_start: 0.8239 (mt0) cc_final: 0.7990 (mt0) REVERT: A 386 ASP cc_start: 0.7497 (m-30) cc_final: 0.7154 (m-30) REVERT: A 393 MET cc_start: 0.8546 (mtp) cc_final: 0.8157 (mtp) REVERT: A 423 ASP cc_start: 0.8063 (m-30) cc_final: 0.7776 (m-30) REVERT: A 474 ASP cc_start: 0.7518 (m-30) cc_final: 0.7274 (m-30) REVERT: A 480 GLU cc_start: 0.7332 (tm-30) cc_final: 0.6919 (tm-30) REVERT: A 566 LYS cc_start: 0.8295 (ttpp) cc_final: 0.8067 (ttpt) REVERT: B 32 ASN cc_start: 0.8000 (t0) cc_final: 0.7350 (t0) REVERT: B 61 LYS cc_start: 0.8073 (pttm) cc_final: 0.7866 (pttm) REVERT: B 71 LEU cc_start: 0.8719 (mt) cc_final: 0.8512 (mp) REVERT: B 95 LEU cc_start: 0.8600 (mm) cc_final: 0.8210 (mp) REVERT: B 136 LYS cc_start: 0.7786 (tptt) cc_final: 0.7136 (tptt) REVERT: B 142 LEU cc_start: 0.8550 (mt) cc_final: 0.8324 (mm) outliers start: 8 outliers final: 6 residues processed: 224 average time/residue: 0.0994 time to fit residues: 27.9909 Evaluate side-chains 225 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 219 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 41 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 33 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.111327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.098506 restraints weight = 9782.845| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.65 r_work: 0.3102 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6367 Z= 0.201 Angle : 0.610 8.943 8647 Z= 0.306 Chirality : 0.044 0.182 970 Planarity : 0.004 0.045 1090 Dihedral : 10.588 136.939 926 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.40 % Allowed : 17.07 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.31), residues: 769 helix: 1.11 (0.31), residues: 296 sheet: 0.31 (0.45), residues: 149 loop : -1.23 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 327 TYR 0.015 0.001 TYR A 41 PHE 0.013 0.001 PHE A 433 TRP 0.010 0.001 TRP A 406 HIS 0.004 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 6367) covalent geometry : angle 0.61018 ( 8647) hydrogen bonds : bond 0.04996 ( 266) hydrogen bonds : angle 4.44350 ( 786) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 220 time to evaluate : 0.234 Fit side-chains REVERT: A 19 LYS cc_start: 0.8602 (tttp) cc_final: 0.8323 (ttmm) REVERT: A 109 CYS cc_start: 0.7915 (m) cc_final: 0.7497 (m) REVERT: A 128 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7185 (tm-30) REVERT: A 246 LYS cc_start: 0.8639 (ptpt) cc_final: 0.8373 (ptpt) REVERT: A 272 MET cc_start: 0.8134 (tmm) cc_final: 0.7859 (tmm) REVERT: A 282 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7421 (mm-30) REVERT: A 316 MET cc_start: 0.8538 (mtt) cc_final: 0.8329 (mtt) REVERT: A 357 GLN cc_start: 0.8259 (mt0) cc_final: 0.7997 (mt0) REVERT: A 377 ARG cc_start: 0.7676 (mmm160) cc_final: 0.7382 (mmm160) REVERT: A 393 MET cc_start: 0.8563 (mtp) cc_final: 0.8142 (mtp) REVERT: A 423 ASP cc_start: 0.8063 (m-30) cc_final: 0.7767 (m-30) REVERT: A 463 LEU cc_start: 0.8463 (pp) cc_final: 0.8193 (pt) REVERT: A 464 GLU cc_start: 0.7492 (pm20) cc_final: 0.7087 (mp0) REVERT: A 474 ASP cc_start: 0.7546 (m-30) cc_final: 0.7292 (m-30) REVERT: A 480 GLU cc_start: 0.7336 (tm-30) cc_final: 0.6927 (tm-30) REVERT: A 566 LYS cc_start: 0.8282 (ttpp) cc_final: 0.8043 (ttpt) REVERT: B 32 ASN cc_start: 0.7923 (t0) cc_final: 0.7312 (t0) REVERT: B 136 LYS cc_start: 0.7712 (tptt) cc_final: 0.7148 (tptt) outliers start: 16 outliers final: 9 residues processed: 226 average time/residue: 0.0914 time to fit residues: 25.8471 Evaluate side-chains 224 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 215 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 154 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.097549 restraints weight = 9918.276| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.66 r_work: 0.3098 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6367 Z= 0.199 Angle : 0.616 9.611 8647 Z= 0.308 Chirality : 0.044 0.173 970 Planarity : 0.004 0.046 1090 Dihedral : 10.641 135.185 926 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.10 % Allowed : 19.61 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.31), residues: 769 helix: 1.23 (0.31), residues: 290 sheet: 0.34 (0.45), residues: 149 loop : -1.22 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 327 TYR 0.011 0.001 TYR A 41 PHE 0.012 0.001 PHE A 433 TRP 0.010 0.001 TRP A 406 HIS 0.003 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 6367) covalent geometry : angle 0.61634 ( 8647) hydrogen bonds : bond 0.04913 ( 266) hydrogen bonds : angle 4.45357 ( 786) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 220 time to evaluate : 0.177 Fit side-chains REVERT: A 19 LYS cc_start: 0.8582 (tttp) cc_final: 0.8284 (ttmm) REVERT: A 65 ASP cc_start: 0.7572 (t0) cc_final: 0.7358 (t0) REVERT: A 109 CYS cc_start: 0.7969 (m) cc_final: 0.7568 (m) REVERT: A 128 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7283 (tm-30) REVERT: A 246 LYS cc_start: 0.8611 (ptpt) cc_final: 0.8320 (ptpt) REVERT: A 272 MET cc_start: 0.8136 (tmm) cc_final: 0.7834 (tmm) REVERT: A 282 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7427 (mm-30) REVERT: A 357 GLN cc_start: 0.8274 (mt0) cc_final: 0.8029 (mt0) REVERT: A 377 ARG cc_start: 0.7709 (mmm160) cc_final: 0.7403 (mmm160) REVERT: A 393 MET cc_start: 0.8495 (mtp) cc_final: 0.8072 (mtp) REVERT: A 423 ASP cc_start: 0.8075 (m-30) cc_final: 0.7758 (m-30) REVERT: A 464 GLU cc_start: 0.7509 (pm20) cc_final: 0.7281 (mp0) REVERT: A 474 ASP cc_start: 0.7590 (m-30) cc_final: 0.7382 (m-30) REVERT: A 480 GLU cc_start: 0.7365 (tm-30) cc_final: 0.7039 (tm-30) REVERT: A 567 GLN cc_start: 0.8237 (tp40) cc_final: 0.7972 (tp40) REVERT: B 32 ASN cc_start: 0.7787 (t0) cc_final: 0.7174 (t0) REVERT: B 136 LYS cc_start: 0.7713 (tptt) cc_final: 0.7258 (tptt) outliers start: 14 outliers final: 13 residues processed: 223 average time/residue: 0.0953 time to fit residues: 26.7452 Evaluate side-chains 232 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 219 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 154 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 0.0370 chunk 14 optimal weight: 0.0980 chunk 8 optimal weight: 0.2980 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.112960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.100265 restraints weight = 9891.280| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.66 r_work: 0.3132 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6367 Z= 0.127 Angle : 0.575 10.202 8647 Z= 0.282 Chirality : 0.041 0.185 970 Planarity : 0.004 0.041 1090 Dihedral : 10.804 135.452 926 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.54 % Allowed : 19.76 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.31), residues: 769 helix: 1.35 (0.32), residues: 290 sheet: 0.26 (0.45), residues: 151 loop : -1.08 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 369 TYR 0.011 0.001 TYR A 329 PHE 0.012 0.001 PHE A 433 TRP 0.009 0.001 TRP A 458 HIS 0.003 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6367) covalent geometry : angle 0.57531 ( 8647) hydrogen bonds : bond 0.04135 ( 266) hydrogen bonds : angle 4.26715 ( 786) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 214 time to evaluate : 0.230 Fit side-chains REVERT: A 19 LYS cc_start: 0.8625 (tttp) cc_final: 0.8364 (ttmm) REVERT: A 65 ASP cc_start: 0.7557 (t0) cc_final: 0.7299 (t0) REVERT: A 109 CYS cc_start: 0.7963 (m) cc_final: 0.7545 (m) REVERT: A 121 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7488 (tp30) REVERT: A 128 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7247 (tm-30) REVERT: A 246 LYS cc_start: 0.8598 (ptpt) cc_final: 0.8322 (ptpt) REVERT: A 272 MET cc_start: 0.8115 (tmm) cc_final: 0.7834 (tmm) REVERT: A 357 GLN cc_start: 0.8219 (mt0) cc_final: 0.8000 (mt0) REVERT: A 377 ARG cc_start: 0.7687 (mmm160) cc_final: 0.7296 (mmm160) REVERT: A 393 MET cc_start: 0.8531 (mtp) cc_final: 0.8098 (mtp) REVERT: A 423 ASP cc_start: 0.8060 (m-30) cc_final: 0.7769 (m-30) REVERT: A 464 GLU cc_start: 0.7474 (pm20) cc_final: 0.7262 (mp0) REVERT: A 474 ASP cc_start: 0.7596 (m-30) cc_final: 0.7383 (m-30) REVERT: A 480 GLU cc_start: 0.7371 (tm-30) cc_final: 0.7066 (tm-30) REVERT: A 598 ASP cc_start: 0.7579 (m-30) cc_final: 0.7252 (m-30) REVERT: B 32 ASN cc_start: 0.7801 (t0) cc_final: 0.7223 (t0) REVERT: B 136 LYS cc_start: 0.7628 (tptt) cc_final: 0.7063 (tptt) REVERT: B 141 LEU cc_start: 0.8702 (mt) cc_final: 0.8498 (mm) outliers start: 17 outliers final: 13 residues processed: 218 average time/residue: 0.0995 time to fit residues: 27.1775 Evaluate side-chains 225 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 154 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.099032 restraints weight = 9850.658| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.64 r_work: 0.3116 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6367 Z= 0.181 Angle : 0.593 10.433 8647 Z= 0.295 Chirality : 0.043 0.184 970 Planarity : 0.004 0.046 1090 Dihedral : 10.931 134.526 926 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.40 % Allowed : 21.71 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.31), residues: 769 helix: 1.34 (0.31), residues: 290 sheet: 0.24 (0.45), residues: 151 loop : -1.08 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 369 TYR 0.009 0.001 TYR A 41 PHE 0.012 0.001 PHE A 433 TRP 0.011 0.001 TRP A 406 HIS 0.003 0.001 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 6367) covalent geometry : angle 0.59320 ( 8647) hydrogen bonds : bond 0.04683 ( 266) hydrogen bonds : angle 4.30816 ( 786) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 219 time to evaluate : 0.239 Fit side-chains REVERT: A 19 LYS cc_start: 0.8594 (tttp) cc_final: 0.8339 (ttmm) REVERT: A 56 SER cc_start: 0.8655 (p) cc_final: 0.8338 (t) REVERT: A 65 ASP cc_start: 0.7630 (t0) cc_final: 0.7316 (t0) REVERT: A 109 CYS cc_start: 0.7977 (m) cc_final: 0.7550 (m) REVERT: A 121 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7492 (tp30) REVERT: A 128 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7276 (tm-30) REVERT: A 157 ASP cc_start: 0.7355 (m-30) cc_final: 0.6906 (m-30) REVERT: A 246 LYS cc_start: 0.8614 (ptpt) cc_final: 0.8340 (ptpt) REVERT: A 272 MET cc_start: 0.8106 (tmm) cc_final: 0.7819 (tmm) REVERT: A 277 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8116 (p) REVERT: A 357 GLN cc_start: 0.8244 (mt0) cc_final: 0.8011 (mt0) REVERT: A 377 ARG cc_start: 0.7675 (mmm160) cc_final: 0.7333 (mmm160) REVERT: A 386 ASP cc_start: 0.7167 (m-30) cc_final: 0.6831 (m-30) REVERT: A 393 MET cc_start: 0.8567 (mtp) cc_final: 0.8137 (mtp) REVERT: A 423 ASP cc_start: 0.8073 (m-30) cc_final: 0.7793 (m-30) REVERT: A 464 GLU cc_start: 0.7429 (pm20) cc_final: 0.7214 (mp0) REVERT: A 474 ASP cc_start: 0.7603 (m-30) cc_final: 0.7393 (m-30) REVERT: A 480 GLU cc_start: 0.7367 (tm-30) cc_final: 0.7049 (tm-30) REVERT: A 598 ASP cc_start: 0.7596 (m-30) cc_final: 0.7284 (m-30) REVERT: B 32 ASN cc_start: 0.8003 (t0) cc_final: 0.7397 (t0) REVERT: B 136 LYS cc_start: 0.7632 (tptt) cc_final: 0.7198 (tptt) outliers start: 16 outliers final: 13 residues processed: 226 average time/residue: 0.0997 time to fit residues: 28.3496 Evaluate side-chains 229 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 215 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 154 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 66 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 0.0470 chunk 67 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.112867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.100252 restraints weight = 9885.579| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.63 r_work: 0.3120 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6367 Z= 0.127 Angle : 0.576 10.729 8647 Z= 0.283 Chirality : 0.041 0.181 970 Planarity : 0.004 0.039 1090 Dihedral : 10.962 134.965 926 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.10 % Allowed : 21.56 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.31), residues: 769 helix: 1.37 (0.31), residues: 291 sheet: 0.34 (0.44), residues: 153 loop : -1.04 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 369 TYR 0.012 0.001 TYR A 329 PHE 0.012 0.001 PHE A 433 TRP 0.009 0.001 TRP A 458 HIS 0.002 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6367) covalent geometry : angle 0.57630 ( 8647) hydrogen bonds : bond 0.04102 ( 266) hydrogen bonds : angle 4.24154 ( 786) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 0.290 Fit side-chains REVERT: A 19 LYS cc_start: 0.8572 (tttp) cc_final: 0.8334 (ttmm) REVERT: A 29 HIS cc_start: 0.6268 (t70) cc_final: 0.6036 (t70) REVERT: A 56 SER cc_start: 0.8639 (p) cc_final: 0.8323 (t) REVERT: A 65 ASP cc_start: 0.7599 (t0) cc_final: 0.7317 (t0) REVERT: A 109 CYS cc_start: 0.7992 (m) cc_final: 0.7558 (m) REVERT: A 121 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7339 (tp30) REVERT: A 128 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7247 (tm-30) REVERT: A 246 LYS cc_start: 0.8593 (ptpt) cc_final: 0.8306 (ptpt) REVERT: A 272 MET cc_start: 0.8079 (tmm) cc_final: 0.7787 (tmm) REVERT: A 276 MET cc_start: 0.8352 (ttp) cc_final: 0.8119 (ttm) REVERT: A 277 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.8075 (p) REVERT: A 357 GLN cc_start: 0.8209 (mt0) cc_final: 0.7993 (mt0) REVERT: A 377 ARG cc_start: 0.7674 (mmm160) cc_final: 0.7314 (mmm160) REVERT: A 386 ASP cc_start: 0.7178 (m-30) cc_final: 0.6895 (m-30) REVERT: A 393 MET cc_start: 0.8544 (mtp) cc_final: 0.8108 (mtp) REVERT: A 463 LEU cc_start: 0.8557 (pt) cc_final: 0.8140 (pp) REVERT: A 464 GLU cc_start: 0.7429 (pm20) cc_final: 0.7224 (mp0) REVERT: A 474 ASP cc_start: 0.7602 (m-30) cc_final: 0.7390 (m-30) REVERT: A 480 GLU cc_start: 0.7368 (tm-30) cc_final: 0.7052 (tm-30) REVERT: A 567 GLN cc_start: 0.8178 (tp40) cc_final: 0.7899 (tp40) REVERT: B 32 ASN cc_start: 0.8030 (t0) cc_final: 0.7500 (t0) REVERT: B 136 LYS cc_start: 0.7626 (tptt) cc_final: 0.7024 (tptt) outliers start: 14 outliers final: 11 residues processed: 215 average time/residue: 0.1011 time to fit residues: 27.3415 Evaluate side-chains 221 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 209 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 154 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 47 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 50 optimal weight: 0.7980 chunk 13 optimal weight: 0.0970 chunk 69 optimal weight: 2.9990 chunk 39 optimal weight: 0.0570 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.113938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.101028 restraints weight = 9908.423| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.68 r_work: 0.3079 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6367 Z= 0.115 Angle : 0.579 11.084 8647 Z= 0.285 Chirality : 0.041 0.186 970 Planarity : 0.004 0.038 1090 Dihedral : 10.945 135.419 926 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.10 % Allowed : 22.60 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.31), residues: 769 helix: 1.42 (0.31), residues: 291 sheet: 0.38 (0.45), residues: 153 loop : -1.02 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 369 TYR 0.009 0.001 TYR A 329 PHE 0.010 0.001 PHE A 433 TRP 0.010 0.001 TRP A 406 HIS 0.002 0.000 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6367) covalent geometry : angle 0.57882 ( 8647) hydrogen bonds : bond 0.03936 ( 266) hydrogen bonds : angle 4.18660 ( 786) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 0.201 Fit side-chains REVERT: A 19 LYS cc_start: 0.8433 (tttp) cc_final: 0.8188 (ttmm) REVERT: A 29 HIS cc_start: 0.6274 (t70) cc_final: 0.6008 (t70) REVERT: A 56 SER cc_start: 0.8658 (p) cc_final: 0.8280 (t) REVERT: A 65 ASP cc_start: 0.7545 (t0) cc_final: 0.7234 (t0) REVERT: A 107 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7952 (ttm-80) REVERT: A 128 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7216 (tm-30) REVERT: A 246 LYS cc_start: 0.8569 (ptpt) cc_final: 0.8282 (ptpt) REVERT: A 272 MET cc_start: 0.8129 (tmm) cc_final: 0.7815 (tmm) REVERT: A 276 MET cc_start: 0.8430 (ttp) cc_final: 0.8165 (ttp) REVERT: A 277 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.8024 (p) REVERT: A 377 ARG cc_start: 0.7733 (mmm160) cc_final: 0.7365 (mmm160) REVERT: A 386 ASP cc_start: 0.7224 (m-30) cc_final: 0.6898 (m-30) REVERT: A 393 MET cc_start: 0.8554 (mtp) cc_final: 0.8152 (mtp) REVERT: A 463 LEU cc_start: 0.8555 (pt) cc_final: 0.8140 (pp) REVERT: A 464 GLU cc_start: 0.7452 (pm20) cc_final: 0.7214 (mp0) REVERT: A 480 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7001 (tm-30) REVERT: B 32 ASN cc_start: 0.7846 (t0) cc_final: 0.7246 (t0) REVERT: B 95 LEU cc_start: 0.8611 (mt) cc_final: 0.8355 (mm) REVERT: B 136 LYS cc_start: 0.7588 (tptt) cc_final: 0.6898 (tptt) outliers start: 14 outliers final: 9 residues processed: 214 average time/residue: 0.0965 time to fit residues: 25.9456 Evaluate side-chains 216 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 205 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 154 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 54 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 chunk 72 optimal weight: 0.0370 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.112658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.099866 restraints weight = 9915.489| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.65 r_work: 0.3121 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6367 Z= 0.145 Angle : 0.603 11.097 8647 Z= 0.294 Chirality : 0.042 0.191 970 Planarity : 0.004 0.038 1090 Dihedral : 10.895 135.367 926 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.80 % Allowed : 23.20 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.31), residues: 769 helix: 1.36 (0.31), residues: 291 sheet: 0.41 (0.45), residues: 153 loop : -1.02 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 369 TYR 0.016 0.001 TYR A 329 PHE 0.011 0.001 PHE A 433 TRP 0.010 0.001 TRP A 406 HIS 0.002 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 6367) covalent geometry : angle 0.60309 ( 8647) hydrogen bonds : bond 0.04269 ( 266) hydrogen bonds : angle 4.21880 ( 786) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 206 time to evaluate : 0.249 Fit side-chains REVERT: A 19 LYS cc_start: 0.8574 (tttp) cc_final: 0.8324 (ttmm) REVERT: A 29 HIS cc_start: 0.6299 (t70) cc_final: 0.6057 (t70) REVERT: A 56 SER cc_start: 0.8638 (p) cc_final: 0.8329 (t) REVERT: A 65 ASP cc_start: 0.7585 (t0) cc_final: 0.7329 (t0) REVERT: A 107 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7998 (ttm-80) REVERT: A 128 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7253 (tm-30) REVERT: A 246 LYS cc_start: 0.8605 (ptpt) cc_final: 0.8333 (ptpt) REVERT: A 272 MET cc_start: 0.8056 (tmm) cc_final: 0.7769 (tmm) REVERT: A 277 THR cc_start: 0.8362 (OUTLIER) cc_final: 0.8106 (p) REVERT: A 377 ARG cc_start: 0.7701 (mmm160) cc_final: 0.7338 (mmm160) REVERT: A 386 ASP cc_start: 0.7160 (m-30) cc_final: 0.6862 (m-30) REVERT: A 393 MET cc_start: 0.8586 (mtp) cc_final: 0.8149 (mtp) REVERT: A 463 LEU cc_start: 0.8562 (pt) cc_final: 0.8194 (pp) REVERT: A 464 GLU cc_start: 0.7409 (pm20) cc_final: 0.7105 (mp0) REVERT: A 474 ASP cc_start: 0.7528 (m-30) cc_final: 0.7277 (m-30) REVERT: A 480 GLU cc_start: 0.7400 (tm-30) cc_final: 0.7071 (tm-30) REVERT: A 567 GLN cc_start: 0.8192 (tp40) cc_final: 0.7923 (tp40) REVERT: B 32 ASN cc_start: 0.7826 (t0) cc_final: 0.7166 (t0) REVERT: B 136 LYS cc_start: 0.7628 (tptt) cc_final: 0.7041 (tptt) REVERT: B 141 LEU cc_start: 0.8627 (mt) cc_final: 0.8400 (mm) REVERT: B 142 LEU cc_start: 0.8523 (mt) cc_final: 0.8289 (mm) outliers start: 12 outliers final: 8 residues processed: 210 average time/residue: 0.0966 time to fit residues: 25.4022 Evaluate side-chains 209 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 199 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 154 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 58 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 22 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.111635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.098774 restraints weight = 9897.872| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.67 r_work: 0.3112 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6367 Z= 0.178 Angle : 0.629 10.965 8647 Z= 0.308 Chirality : 0.043 0.190 970 Planarity : 0.004 0.040 1090 Dihedral : 10.903 135.265 926 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.65 % Allowed : 23.20 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.31), residues: 769 helix: 1.29 (0.31), residues: 291 sheet: 0.39 (0.46), residues: 151 loop : -1.04 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 369 TYR 0.018 0.002 TYR A 329 PHE 0.012 0.001 PHE A 433 TRP 0.011 0.001 TRP B 14 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 6367) covalent geometry : angle 0.62885 ( 8647) hydrogen bonds : bond 0.04595 ( 266) hydrogen bonds : angle 4.30007 ( 786) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 214 time to evaluate : 0.199 Fit side-chains REVERT: A 19 LYS cc_start: 0.8568 (tttp) cc_final: 0.8318 (ttmm) REVERT: A 29 HIS cc_start: 0.6339 (t70) cc_final: 0.6084 (t70) REVERT: A 56 SER cc_start: 0.8645 (p) cc_final: 0.8328 (t) REVERT: A 65 ASP cc_start: 0.7629 (t0) cc_final: 0.7345 (t0) REVERT: A 109 CYS cc_start: 0.7945 (m) cc_final: 0.7501 (m) REVERT: A 128 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7269 (tm-30) REVERT: A 157 ASP cc_start: 0.7335 (m-30) cc_final: 0.6901 (m-30) REVERT: A 246 LYS cc_start: 0.8609 (ptpt) cc_final: 0.8363 (ptpt) REVERT: A 272 MET cc_start: 0.8080 (tmm) cc_final: 0.7787 (tmm) REVERT: A 277 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8111 (p) REVERT: A 377 ARG cc_start: 0.7717 (mmm160) cc_final: 0.7369 (mmm160) REVERT: A 386 ASP cc_start: 0.7171 (m-30) cc_final: 0.6868 (m-30) REVERT: A 393 MET cc_start: 0.8590 (mtp) cc_final: 0.8152 (mtp) REVERT: A 463 LEU cc_start: 0.8564 (pt) cc_final: 0.8193 (pp) REVERT: A 464 GLU cc_start: 0.7419 (pm20) cc_final: 0.7107 (mp0) REVERT: A 474 ASP cc_start: 0.7532 (m-30) cc_final: 0.7275 (m-30) REVERT: A 480 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7083 (tm-30) REVERT: A 567 GLN cc_start: 0.8188 (tp40) cc_final: 0.7855 (tp40) REVERT: B 32 ASN cc_start: 0.7880 (t0) cc_final: 0.7260 (t0) REVERT: B 136 LYS cc_start: 0.7656 (tptt) cc_final: 0.7046 (tptt) REVERT: B 141 LEU cc_start: 0.8687 (mt) cc_final: 0.8464 (mm) outliers start: 11 outliers final: 8 residues processed: 217 average time/residue: 0.1032 time to fit residues: 28.0141 Evaluate side-chains 222 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 213 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 154 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 49 optimal weight: 0.0030 chunk 73 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 0.0570 overall best weight: 0.3908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.112723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.099963 restraints weight = 9818.752| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.64 r_work: 0.3135 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6367 Z= 0.131 Angle : 0.605 10.939 8647 Z= 0.297 Chirality : 0.042 0.192 970 Planarity : 0.004 0.039 1090 Dihedral : 10.953 135.628 926 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.50 % Allowed : 23.50 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.31), residues: 769 helix: 1.32 (0.31), residues: 291 sheet: 0.48 (0.46), residues: 143 loop : -1.02 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 369 TYR 0.018 0.001 TYR A 329 PHE 0.011 0.001 PHE A 433 TRP 0.012 0.001 TRP B 14 HIS 0.002 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6367) covalent geometry : angle 0.60528 ( 8647) hydrogen bonds : bond 0.04084 ( 266) hydrogen bonds : angle 4.22435 ( 786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1477.28 seconds wall clock time: 26 minutes 0.19 seconds (1560.19 seconds total)