Starting phenix.real_space_refine on Tue Jan 14 08:20:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9y_45376/01_2025/9c9y_45376_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9y_45376/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9c9y_45376/01_2025/9c9y_45376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9y_45376/01_2025/9c9y_45376.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9y_45376/01_2025/9c9y_45376_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9y_45376/01_2025/9c9y_45376_neut.cif" } resolution = 3.35 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= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 4.48, per 1000 atoms: 0.72 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: 1.76 Conformation dependent library (CDL) restraints added in 783.3 milliseconds 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: 1.75 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: 1.83 Time building geometry restraints manager: 1.93 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: 3.280 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.810 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.390 ------------------------------------------------------------------------------- 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= 0.355 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 (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: -0.01 (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 TRP 0.008 0.001 TRP A 73 HIS 0.003 0.001 HIS B 156 PHE 0.014 0.002 PHE A 200 TYR 0.011 0.001 TYR A 549 ARG 0.004 0.000 ARG A 369 *********************** 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 : 0.684 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: 0.2383 time to fit residues: 68.0926 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 : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.111981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.099341 restraints weight = 9702.733| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.60 r_work: 0.3121 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.0964 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= 0.281 Angle : 0.617 8.363 8647 Z= 0.310 Chirality : 0.043 0.180 970 Planarity : 0.004 0.046 1090 Dihedral : 10.659 140.400 926 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.20 % Allowed : 13.62 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.31), residues: 769 helix: 1.12 (0.31), residues: 296 sheet: 0.35 (0.45), residues: 151 loop : -1.19 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 406 HIS 0.006 0.001 HIS A 517 PHE 0.015 0.001 PHE A 433 TYR 0.012 0.001 TYR A 329 ARG 0.005 0.000 ARG B 77 *********************** 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 227 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 219 time to evaluate : 0.665 Fit side-chains REVERT: A 19 LYS cc_start: 0.8585 (tttp) cc_final: 0.8222 (ttmm) REVERT: A 26 LEU cc_start: 0.7828 (mp) cc_final: 0.7627 (mt) REVERT: A 65 ASP cc_start: 0.7669 (t0) cc_final: 0.7460 (t0) REVERT: A 109 CYS cc_start: 0.7901 (m) cc_final: 0.7491 (m) REVERT: A 119 ASP cc_start: 0.7344 (p0) cc_final: 0.7139 (p0) REVERT: A 128 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7060 (tm-30) REVERT: A 246 LYS cc_start: 0.8599 (ptpt) cc_final: 0.8349 (ptpt) REVERT: A 272 MET cc_start: 0.8107 (tmm) cc_final: 0.7818 (tmm) REVERT: A 282 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7383 (mm-30) REVERT: A 357 GLN cc_start: 0.8238 (mt0) cc_final: 0.7987 (mt0) REVERT: A 386 ASP cc_start: 0.7487 (m-30) cc_final: 0.7086 (m-30) REVERT: A 393 MET cc_start: 0.8532 (mtp) cc_final: 0.8142 (mtp) REVERT: A 423 ASP cc_start: 0.8055 (m-30) cc_final: 0.7768 (m-30) REVERT: A 464 GLU cc_start: 0.7470 (pm20) cc_final: 0.7197 (mp0) REVERT: A 474 ASP cc_start: 0.7517 (m-30) cc_final: 0.7280 (m-30) REVERT: A 480 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6912 (tm-30) REVERT: A 566 LYS cc_start: 0.8280 (ttpp) cc_final: 0.8051 (ttpt) REVERT: B 32 ASN cc_start: 0.7989 (t0) cc_final: 0.7344 (t0) REVERT: B 61 LYS cc_start: 0.8076 (pttm) cc_final: 0.7863 (pttm) REVERT: B 136 LYS cc_start: 0.7745 (tptt) cc_final: 0.7160 (tptt) outliers start: 8 outliers final: 6 residues processed: 221 average time/residue: 0.2241 time to fit residues: 61.9758 Evaluate side-chains 219 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 213 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 A residue 442 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 16 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 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 275 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.111821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.098966 restraints weight = 9792.317| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.65 r_work: 0.3109 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1202 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= 0.265 Angle : 0.588 8.595 8647 Z= 0.295 Chirality : 0.043 0.174 970 Planarity : 0.004 0.044 1090 Dihedral : 10.583 137.323 926 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.54 % Allowed : 17.07 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.31), residues: 769 helix: 1.13 (0.31), residues: 296 sheet: 0.36 (0.45), residues: 149 loop : -1.21 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 406 HIS 0.004 0.001 HIS A 517 PHE 0.012 0.001 PHE A 433 TYR 0.015 0.001 TYR A 41 ARG 0.003 0.000 ARG A 327 *********************** 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 232 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 215 time to evaluate : 0.720 Fit side-chains REVERT: A 19 LYS cc_start: 0.8596 (tttp) cc_final: 0.8234 (ttmm) REVERT: A 109 CYS cc_start: 0.7904 (m) cc_final: 0.7491 (m) REVERT: A 119 ASP cc_start: 0.7323 (p0) cc_final: 0.7110 (p0) REVERT: A 128 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7168 (tm-30) REVERT: A 246 LYS cc_start: 0.8615 (ptpt) cc_final: 0.8348 (ptpt) REVERT: A 282 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7410 (mm-30) REVERT: A 316 MET cc_start: 0.8524 (mtt) cc_final: 0.8321 (mtt) REVERT: A 357 GLN cc_start: 0.8252 (mt0) cc_final: 0.7999 (mt0) REVERT: A 377 ARG cc_start: 0.7668 (mmm160) cc_final: 0.7374 (mmm160) REVERT: A 393 MET cc_start: 0.8558 (mtp) cc_final: 0.8142 (mtp) REVERT: A 423 ASP cc_start: 0.8056 (m-30) cc_final: 0.7767 (m-30) REVERT: A 464 GLU cc_start: 0.7398 (pm20) cc_final: 0.7122 (mp0) REVERT: A 474 ASP cc_start: 0.7537 (m-30) cc_final: 0.7282 (m-30) REVERT: A 480 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6961 (tm-30) REVERT: B 32 ASN cc_start: 0.7919 (t0) cc_final: 0.7291 (t0) REVERT: B 136 LYS cc_start: 0.7730 (tptt) cc_final: 0.7274 (tptt) outliers start: 17 outliers final: 9 residues processed: 221 average time/residue: 0.2214 time to fit residues: 61.1629 Evaluate side-chains 218 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 209 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 281 LYS 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 43 optimal weight: 0.8980 chunk 76 optimal weight: 0.0570 chunk 48 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 70 optimal weight: 0.0970 chunk 17 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 44 optimal weight: 0.0030 overall best weight: 0.2506 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.113353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.100281 restraints weight = 10067.372| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.72 r_work: 0.3138 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6367 Z= 0.159 Angle : 0.567 9.599 8647 Z= 0.279 Chirality : 0.041 0.176 970 Planarity : 0.004 0.042 1090 Dihedral : 10.636 137.534 926 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.10 % Allowed : 18.26 % Favored : 79.64 % 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: 0.19 (0.31), residues: 769 helix: 1.33 (0.31), residues: 291 sheet: 0.40 (0.46), residues: 144 loop : -1.07 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 406 HIS 0.003 0.000 HIS A 517 PHE 0.010 0.001 PHE A 433 TYR 0.008 0.001 TYR A 411 ARG 0.003 0.000 ARG B 77 *********************** 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 220 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 0.682 Fit side-chains REVERT: A 19 LYS cc_start: 0.8492 (tttp) cc_final: 0.8234 (ttmm) REVERT: A 26 LEU cc_start: 0.7799 (mp) cc_final: 0.7592 (mt) REVERT: A 65 ASP cc_start: 0.7590 (t0) cc_final: 0.7380 (t0) REVERT: A 119 ASP cc_start: 0.7222 (p0) cc_final: 0.6957 (p0) REVERT: A 128 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7223 (tm-30) REVERT: A 246 LYS cc_start: 0.8587 (ptpt) cc_final: 0.8172 (ptpt) REVERT: A 272 MET cc_start: 0.8097 (tmm) cc_final: 0.7802 (tmm) REVERT: A 357 GLN cc_start: 0.8168 (mt0) cc_final: 0.7954 (mt0) REVERT: A 377 ARG cc_start: 0.7693 (mmm160) cc_final: 0.7377 (mmm160) REVERT: A 393 MET cc_start: 0.8484 (mtp) cc_final: 0.8062 (mtp) REVERT: A 598 ASP cc_start: 0.7626 (m-30) cc_final: 0.7367 (m-30) REVERT: B 32 ASN cc_start: 0.8005 (t0) cc_final: 0.7393 (t0) REVERT: B 136 LYS cc_start: 0.7614 (tptt) cc_final: 0.7044 (tptt) outliers start: 14 outliers final: 11 residues processed: 211 average time/residue: 0.2372 time to fit residues: 63.3990 Evaluate side-chains 213 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 35 optimal weight: 0.0570 chunk 30 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 39 optimal weight: 0.0980 overall best weight: 0.6302 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.110899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.098207 restraints weight = 10025.084| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.69 r_work: 0.3109 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1529 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= 0.268 Angle : 0.598 10.195 8647 Z= 0.296 Chirality : 0.043 0.184 970 Planarity : 0.004 0.043 1090 Dihedral : 10.655 135.721 926 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.10 % Allowed : 20.21 % 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 (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: 0.10 (0.31), residues: 769 helix: 1.22 (0.31), residues: 296 sheet: 0.25 (0.45), residues: 151 loop : -1.10 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 406 HIS 0.003 0.001 HIS A 517 PHE 0.011 0.001 PHE A 433 TYR 0.014 0.001 TYR A 329 ARG 0.006 0.000 ARG A 369 *********************** 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 228 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 214 time to evaluate : 0.643 Fit side-chains REVERT: A 19 LYS cc_start: 0.8501 (tttp) cc_final: 0.8246 (ttmm) REVERT: A 56 SER cc_start: 0.8665 (p) cc_final: 0.8341 (t) REVERT: A 65 ASP cc_start: 0.7590 (t0) cc_final: 0.7282 (t0) REVERT: A 109 CYS cc_start: 0.8007 (m) cc_final: 0.7585 (m) REVERT: A 119 ASP cc_start: 0.7098 (p0) cc_final: 0.6752 (p0) REVERT: A 128 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7282 (tm-30) REVERT: A 157 ASP cc_start: 0.7461 (m-30) cc_final: 0.7011 (m-30) REVERT: A 246 LYS cc_start: 0.8600 (ptpt) cc_final: 0.8365 (ptpt) REVERT: A 272 MET cc_start: 0.8124 (tmm) cc_final: 0.7875 (tmm) REVERT: A 277 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8153 (p) REVERT: A 357 GLN cc_start: 0.8241 (mt0) cc_final: 0.8011 (mt0) REVERT: A 377 ARG cc_start: 0.7737 (mmm160) cc_final: 0.7421 (mmm160) REVERT: A 386 ASP cc_start: 0.7117 (m-30) cc_final: 0.6795 (m-30) REVERT: A 393 MET cc_start: 0.8515 (mtp) cc_final: 0.8062 (mtp) REVERT: A 423 ASP cc_start: 0.8053 (m-30) cc_final: 0.7772 (m-30) REVERT: A 463 LEU cc_start: 0.8476 (pp) cc_final: 0.8239 (pt) REVERT: A 464 GLU cc_start: 0.7425 (pm20) cc_final: 0.7061 (mp0) REVERT: A 474 ASP cc_start: 0.7559 (m-30) cc_final: 0.7296 (m-30) REVERT: A 598 ASP cc_start: 0.7681 (m-30) cc_final: 0.7413 (m-30) REVERT: B 32 ASN cc_start: 0.8004 (t0) cc_final: 0.7395 (t0) REVERT: B 136 LYS cc_start: 0.7715 (tptt) cc_final: 0.7156 (tptt) outliers start: 14 outliers final: 12 residues processed: 218 average time/residue: 0.2285 time to fit residues: 61.8948 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 : 0.760 ------------------------------------------------------------------------------- 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 256 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 277 THR 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 55 SER 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 26 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.110395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.097741 restraints weight = 9916.580| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.65 r_work: 0.3101 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6367 Z= 0.305 Angle : 0.606 10.277 8647 Z= 0.301 Chirality : 0.044 0.184 970 Planarity : 0.004 0.044 1090 Dihedral : 10.952 134.381 926 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.40 % Allowed : 20.06 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.31), residues: 769 helix: 1.30 (0.31), residues: 290 sheet: 0.26 (0.45), residues: 151 loop : -1.13 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 406 HIS 0.003 0.001 HIS B 103 PHE 0.015 0.001 PHE A 433 TYR 0.015 0.001 TYR A 329 ARG 0.003 0.000 ARG A 369 *********************** 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 : 0.643 Fit side-chains REVERT: A 19 LYS cc_start: 0.8594 (tttp) cc_final: 0.8314 (ttmm) REVERT: A 56 SER cc_start: 0.8672 (p) cc_final: 0.8348 (t) REVERT: A 65 ASP cc_start: 0.7675 (t0) cc_final: 0.7380 (t0) REVERT: A 69 LYS cc_start: 0.8613 (tptm) cc_final: 0.8394 (tptp) REVERT: A 109 CYS cc_start: 0.8030 (m) cc_final: 0.7608 (m) REVERT: A 119 ASP cc_start: 0.6916 (p0) cc_final: 0.6664 (p0) REVERT: A 128 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7305 (tm-30) REVERT: A 157 ASP cc_start: 0.7374 (m-30) cc_final: 0.6919 (m-30) REVERT: A 246 LYS cc_start: 0.8651 (ptpt) cc_final: 0.8399 (ptpt) REVERT: A 272 MET cc_start: 0.8148 (tmm) cc_final: 0.7906 (tmm) REVERT: A 277 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8155 (p) REVERT: A 357 GLN cc_start: 0.8261 (mt0) cc_final: 0.8010 (mt0) REVERT: A 377 ARG cc_start: 0.7758 (mmm160) cc_final: 0.7417 (mmm160) REVERT: A 386 ASP cc_start: 0.7059 (m-30) cc_final: 0.6740 (m-30) REVERT: A 393 MET cc_start: 0.8503 (mtp) cc_final: 0.8057 (mtp) REVERT: A 423 ASP cc_start: 0.8092 (m-30) cc_final: 0.7795 (m-30) REVERT: A 464 GLU cc_start: 0.7430 (pm20) cc_final: 0.7217 (mp0) REVERT: A 474 ASP cc_start: 0.7543 (m-30) cc_final: 0.7279 (m-30) REVERT: A 567 GLN cc_start: 0.8237 (tp40) cc_final: 0.7923 (tp40) REVERT: A 584 HIS cc_start: 0.7494 (t-90) cc_final: 0.7261 (t-90) REVERT: A 598 ASP cc_start: 0.7703 (m-30) cc_final: 0.7471 (m-30) REVERT: B 32 ASN cc_start: 0.7810 (t0) cc_final: 0.7355 (t0) REVERT: B 136 LYS cc_start: 0.7729 (tptt) cc_final: 0.7136 (tptt) REVERT: B 141 LEU cc_start: 0.8619 (mm) cc_final: 0.8326 (mt) outliers start: 16 outliers final: 14 residues processed: 224 average time/residue: 0.2172 time to fit residues: 60.9963 Evaluate side-chains 237 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 222 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 55 SER 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 48 optimal weight: 0.8980 chunk 45 optimal weight: 0.0980 chunk 65 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.110750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.097975 restraints weight = 9933.859| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.66 r_work: 0.3103 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6367 Z= 0.267 Angle : 0.604 10.316 8647 Z= 0.299 Chirality : 0.043 0.187 970 Planarity : 0.004 0.048 1090 Dihedral : 10.989 134.131 926 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.84 % Allowed : 20.66 % Favored : 76.50 % 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: 0.10 (0.31), residues: 769 helix: 1.29 (0.31), residues: 290 sheet: 0.27 (0.45), residues: 151 loop : -1.14 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 458 HIS 0.003 0.001 HIS B 103 PHE 0.012 0.001 PHE A 433 TYR 0.016 0.001 TYR A 329 ARG 0.003 0.000 ARG A 369 *********************** 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 233 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 0.608 Fit side-chains REVERT: A 19 LYS cc_start: 0.8586 (tttp) cc_final: 0.8329 (ttmm) REVERT: A 29 HIS cc_start: 0.6361 (t70) cc_final: 0.6119 (t70) REVERT: A 56 SER cc_start: 0.8666 (p) cc_final: 0.8359 (t) REVERT: A 65 ASP cc_start: 0.7552 (t0) cc_final: 0.7285 (t0) REVERT: A 69 LYS cc_start: 0.8622 (tptm) cc_final: 0.8403 (tptp) REVERT: A 109 CYS cc_start: 0.8001 (m) cc_final: 0.7594 (m) REVERT: A 119 ASP cc_start: 0.6823 (p0) cc_final: 0.6591 (p0) REVERT: A 128 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7310 (tm-30) REVERT: A 157 ASP cc_start: 0.7381 (m-30) cc_final: 0.6938 (m-30) REVERT: A 246 LYS cc_start: 0.8635 (ptpt) cc_final: 0.8384 (ptpt) REVERT: A 272 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7840 (tmm) REVERT: A 277 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8160 (p) REVERT: A 357 GLN cc_start: 0.8253 (mt0) cc_final: 0.8031 (mt0) REVERT: A 377 ARG cc_start: 0.7716 (mmm160) cc_final: 0.7371 (mmm160) REVERT: A 386 ASP cc_start: 0.7109 (m-30) cc_final: 0.6810 (m-30) REVERT: A 393 MET cc_start: 0.8493 (mtp) cc_final: 0.8053 (mtp) REVERT: A 423 ASP cc_start: 0.8076 (m-30) cc_final: 0.7788 (m-30) REVERT: A 464 GLU cc_start: 0.7410 (pm20) cc_final: 0.7197 (mp0) REVERT: A 474 ASP cc_start: 0.7557 (m-30) cc_final: 0.7292 (m-30) REVERT: A 567 GLN cc_start: 0.8215 (tp40) cc_final: 0.7893 (tp40) REVERT: A 584 HIS cc_start: 0.7466 (t-90) cc_final: 0.7258 (t-90) REVERT: B 32 ASN cc_start: 0.7738 (t0) cc_final: 0.7100 (t0) REVERT: B 136 LYS cc_start: 0.7683 (tptt) cc_final: 0.7230 (tptt) outliers start: 19 outliers final: 15 residues processed: 221 average time/residue: 0.2232 time to fit residues: 61.5292 Evaluate side-chains 227 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 96 LEU 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 272 MET 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 A residue 556 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 55 SER 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 68 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 26 optimal weight: 0.0980 chunk 57 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.111955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.099269 restraints weight = 9793.553| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.63 r_work: 0.3111 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1700 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= 0.233 Angle : 0.593 10.815 8647 Z= 0.294 Chirality : 0.042 0.185 970 Planarity : 0.004 0.043 1090 Dihedral : 10.969 134.505 926 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.69 % Allowed : 21.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.31), residues: 769 helix: 1.33 (0.31), residues: 290 sheet: 0.27 (0.45), residues: 151 loop : -1.10 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 406 HIS 0.003 0.001 HIS B 103 PHE 0.014 0.001 PHE A 433 TYR 0.016 0.001 TYR A 329 ARG 0.003 0.000 ARG A 369 *********************** 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 231 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 0.688 Fit side-chains REVERT: A 19 LYS cc_start: 0.8589 (tttp) cc_final: 0.8351 (ttmm) REVERT: A 29 HIS cc_start: 0.6309 (t70) cc_final: 0.6069 (t70) REVERT: A 109 CYS cc_start: 0.7948 (m) cc_final: 0.7567 (m) REVERT: A 119 ASP cc_start: 0.6769 (p0) cc_final: 0.6542 (p0) REVERT: A 128 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7244 (tm-30) REVERT: A 157 ASP cc_start: 0.7296 (m-30) cc_final: 0.6844 (m-30) REVERT: A 246 LYS cc_start: 0.8646 (ptpt) cc_final: 0.8388 (ptpt) REVERT: A 272 MET cc_start: 0.8127 (tmm) cc_final: 0.7887 (tmm) REVERT: A 276 MET cc_start: 0.8371 (ttp) cc_final: 0.8157 (ttp) REVERT: A 277 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8105 (p) REVERT: A 357 GLN cc_start: 0.8228 (mt0) cc_final: 0.8002 (mt0) REVERT: A 377 ARG cc_start: 0.7690 (mmm160) cc_final: 0.7325 (mmm160) REVERT: A 386 ASP cc_start: 0.7157 (m-30) cc_final: 0.6870 (m-30) REVERT: A 393 MET cc_start: 0.8550 (mtp) cc_final: 0.8115 (mtp) REVERT: A 464 GLU cc_start: 0.7370 (pm20) cc_final: 0.7151 (mp0) REVERT: A 474 ASP cc_start: 0.7533 (m-30) cc_final: 0.7271 (m-30) REVERT: A 567 GLN cc_start: 0.8185 (tp40) cc_final: 0.7856 (tp40) REVERT: B 32 ASN cc_start: 0.7813 (t0) cc_final: 0.7173 (t0) REVERT: B 136 LYS cc_start: 0.7673 (tptt) cc_final: 0.7065 (tptt) outliers start: 18 outliers final: 15 residues processed: 218 average time/residue: 0.2127 time to fit residues: 57.8209 Evaluate side-chains 225 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 96 LEU Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 179 ASP 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 560 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 55 SER 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 6 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.0670 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.111950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.099332 restraints weight = 9838.455| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.63 r_work: 0.3123 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6367 Z= 0.225 Angle : 0.604 11.159 8647 Z= 0.299 Chirality : 0.042 0.192 970 Planarity : 0.004 0.040 1090 Dihedral : 10.953 134.829 926 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.69 % Allowed : 21.56 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.31), residues: 769 helix: 1.31 (0.31), residues: 291 sheet: 0.29 (0.45), residues: 151 loop : -1.08 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 406 HIS 0.002 0.001 HIS B 103 PHE 0.013 0.001 PHE A 433 TYR 0.017 0.001 TYR A 329 ARG 0.003 0.000 ARG A 369 *********************** 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 224 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 0.737 Fit side-chains REVERT: A 19 LYS cc_start: 0.8548 (tttp) cc_final: 0.8294 (ttmm) REVERT: A 29 HIS cc_start: 0.6315 (t70) cc_final: 0.6075 (t70) REVERT: A 56 SER cc_start: 0.8652 (p) cc_final: 0.8345 (t) REVERT: A 109 CYS cc_start: 0.8010 (m) cc_final: 0.7593 (m) REVERT: A 119 ASP cc_start: 0.6736 (p0) cc_final: 0.6515 (p0) REVERT: A 128 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7243 (tm-30) REVERT: A 157 ASP cc_start: 0.7325 (m-30) cc_final: 0.6876 (m-30) REVERT: A 246 LYS cc_start: 0.8625 (ptpt) cc_final: 0.8376 (ptpt) REVERT: A 272 MET cc_start: 0.8130 (tmm) cc_final: 0.7881 (tmm) REVERT: A 277 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.8128 (p) REVERT: A 357 GLN cc_start: 0.8235 (mt0) cc_final: 0.8019 (mt0) REVERT: A 377 ARG cc_start: 0.7685 (mmm160) cc_final: 0.7330 (mmm160) REVERT: A 386 ASP cc_start: 0.7140 (m-30) cc_final: 0.6845 (m-30) REVERT: A 393 MET cc_start: 0.8581 (mtp) cc_final: 0.8155 (mtp) REVERT: A 464 GLU cc_start: 0.7371 (pm20) cc_final: 0.7143 (mp0) REVERT: A 474 ASP cc_start: 0.7546 (m-30) cc_final: 0.7286 (m-30) REVERT: A 567 GLN cc_start: 0.8181 (tp40) cc_final: 0.7903 (tp40) REVERT: B 32 ASN cc_start: 0.7869 (t0) cc_final: 0.7259 (t0) REVERT: B 136 LYS cc_start: 0.7663 (tptt) cc_final: 0.7085 (tptt) outliers start: 18 outliers final: 15 residues processed: 212 average time/residue: 0.2350 time to fit residues: 62.1544 Evaluate side-chains 221 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 96 LEU Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 179 ASP 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 560 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 55 SER 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 12 optimal weight: 0.6980 chunk 4 optimal weight: 0.0980 chunk 69 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 48 optimal weight: 0.0000 chunk 62 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.112611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.099714 restraints weight = 10015.214| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.68 r_work: 0.3125 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 : 0.003 0.039 6367 Z= 0.215 Angle : 0.601 11.256 8647 Z= 0.297 Chirality : 0.042 0.190 970 Planarity : 0.004 0.041 1090 Dihedral : 10.947 135.208 926 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.25 % Allowed : 22.16 % Favored : 75.60 % 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: 0.19 (0.31), residues: 769 helix: 1.32 (0.31), residues: 291 sheet: 0.33 (0.45), residues: 153 loop : -1.07 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 406 HIS 0.002 0.001 HIS B 103 PHE 0.012 0.001 PHE A 433 TYR 0.017 0.001 TYR A 329 ARG 0.003 0.000 ARG A 369 ********************** 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 222 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 207 time to evaluate : 0.669 Fit side-chains REVERT: A 19 LYS cc_start: 0.8571 (tttp) cc_final: 0.8312 (ttmm) REVERT: A 29 HIS cc_start: 0.6302 (t70) cc_final: 0.6060 (t70) REVERT: A 56 SER cc_start: 0.8671 (p) cc_final: 0.8349 (t) REVERT: A 109 CYS cc_start: 0.7941 (m) cc_final: 0.7591 (m) REVERT: A 119 ASP cc_start: 0.6745 (p0) cc_final: 0.6522 (p0) REVERT: A 128 GLU cc_start: 0.7522 (tm-30) cc_final: 0.7251 (tm-30) REVERT: A 157 ASP cc_start: 0.7288 (m-30) cc_final: 0.6840 (m-30) REVERT: A 246 LYS cc_start: 0.8624 (ptpt) cc_final: 0.8374 (ptpt) REVERT: A 272 MET cc_start: 0.8110 (tmm) cc_final: 0.7852 (tmm) REVERT: A 277 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.8116 (p) REVERT: A 357 GLN cc_start: 0.8215 (mt0) cc_final: 0.7996 (mt0) REVERT: A 377 ARG cc_start: 0.7694 (mmm160) cc_final: 0.7316 (mmm160) REVERT: A 386 ASP cc_start: 0.7120 (m-30) cc_final: 0.6865 (m-30) REVERT: A 393 MET cc_start: 0.8553 (mtp) cc_final: 0.8124 (mtp) REVERT: A 464 GLU cc_start: 0.7363 (pm20) cc_final: 0.7131 (mp0) REVERT: A 474 ASP cc_start: 0.7550 (m-30) cc_final: 0.7291 (m-30) REVERT: A 567 GLN cc_start: 0.8181 (tp40) cc_final: 0.7850 (tp40) REVERT: B 32 ASN cc_start: 0.7904 (t0) cc_final: 0.7280 (t0) REVERT: B 136 LYS cc_start: 0.7645 (tptt) cc_final: 0.7042 (tptt) outliers start: 15 outliers final: 13 residues processed: 211 average time/residue: 0.2240 time to fit residues: 58.9635 Evaluate side-chains 221 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 207 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 96 LEU Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 179 ASP 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 560 ILE 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 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 46 optimal weight: 0.0010 chunk 65 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 0.0030 chunk 21 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 20 optimal weight: 0.0060 chunk 7 optimal weight: 0.5980 overall best weight: 0.2612 ------------------------------------------------------------------------------- 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 = 0.113956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.100972 restraints weight = 9970.742| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.71 r_work: 0.3148 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6367 Z= 0.165 Angle : 0.581 11.263 8647 Z= 0.286 Chirality : 0.041 0.187 970 Planarity : 0.004 0.039 1090 Dihedral : 10.983 135.813 926 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.10 % Allowed : 22.90 % 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 (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: 0.28 (0.31), residues: 769 helix: 1.38 (0.31), residues: 291 sheet: 0.40 (0.46), residues: 143 loop : -0.98 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 406 HIS 0.002 0.000 HIS A 517 PHE 0.012 0.001 PHE A 433 TYR 0.016 0.001 TYR A 329 ARG 0.003 0.000 ARG A 369 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2913.29 seconds wall clock time: 52 minutes 47.67 seconds (3167.67 seconds total)