Starting phenix.real_space_refine on Tue Aug 4 19:01:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9y_45376/08_2026/9c9y_45376_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9y_45376/08_2026/9c9y_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_45376/08_2026/9c9y_45376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9y_45376/08_2026/9c9y_45376.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9y_45376/08_2026/9c9y_45376_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9y_45376/08_2026/9c9y_45376_neut.cif" } 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-2.2rc3-6140/lib/python3.11/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: 1.61, per 1000 atoms: 0.26 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: 0.61 Conformation dependent library (CDL) restraints added in 435.9 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: 0.58 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: 1.03 Time building geometry restraints manager: 0.83 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 1.20e-02 6.94e+03 1.79e+01 bond pdb=" O3' DA C 2 " pdb=" P DA C 3 " ideal model delta sigma weight residual 1.607 1.559 0.048 1.20e-02 6.94e+03 1.60e+01 bond pdb=" O3' DC C 0 " pdb=" P DT C 1 " ideal model delta sigma weight residual 1.607 1.572 0.035 1.20e-02 6.94e+03 8.35e+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=" O4' DT C 6 " pdb=" C1' DT C 6 " ideal model delta sigma weight residual 1.420 1.399 0.021 1.10e-02 8.26e+03 3.79e+00 ... (remaining 6362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 8371 1.58 - 3.15: 223 3.15 - 4.73: 31 4.73 - 6.31: 18 6.31 - 7.89: 4 Bond angle restraints: 8647 Sorted by residual: 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=" C3' DT C 6 " pdb=" C2' DT C 6 " pdb=" C1' DT C 6 " ideal model delta sigma weight residual 102.50 105.56 -3.06 1.20e+00 6.94e-01 6.50e+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 angle pdb=" CB ARG A 377 " pdb=" CG ARG A 377 " pdb=" CD ARG A 377 " ideal model delta sigma weight residual 111.30 117.10 -5.80 2.30e+00 1.89e-01 6.35e+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: 574 0.033 - 0.066: 272 0.066 - 0.100: 82 0.100 - 0.133: 38 0.133 - 0.166: 4 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=" C3' DT C 6 " pdb=" C4' DT C 6 " pdb=" O3' DT C 6 " pdb=" C2' DT C 6 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.25e-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 ... (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: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.230 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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= 0.253 Angle : 0.656 7.886 8647 Z= 0.337 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 are 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/Z covalent geometry : bond 0.00534 / 0.25 ( 6367) covalent geometry : angle 0.65622 / 0.34 ( 8647) hydrogen bonds : bond 0.09483 / 6.67 ( 266) hydrogen bonds : angle 4.94655 / 3.32 ( 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 : 0.176 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: 0.0908 time to fit residues: 26.0214 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 : 0.219 ------------------------------------------------------------------------------- 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... A 275 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.111877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.099124 restraints weight = 9909.404| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.64 r_work: 0.3118 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6367 Z= 0.185 Angle : 0.624 8.256 8647 Z= 0.315 Chirality : 0.043 0.159 970 Planarity : 0.004 0.046 1090 Dihedral : 10.715 141.950 926 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.20 % Allowed : 14.22 % Favored : 84.58 % 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 are not related in a simple way. whole: 0.02 (0.31), residues: 769 helix: 1.15 (0.31), residues: 296 sheet: 0.32 (0.45), residues: 151 loop : -1.21 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 77 TYR 0.012 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/Z covalent geometry : bond 0.00424 / 0.19 ( 6367) covalent geometry : angle 0.62448 / 0.32 ( 8647) hydrogen bonds : bond 0.05148 / 3.40 ( 266) hydrogen bonds : angle 4.60741 / 3.15 ( 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 227 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 219 time to evaluate : 0.134 Fit side-chains REVERT: A 109 CYS cc_start: 0.7895 (m) cc_final: 0.7507 (m) REVERT: A 128 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7079 (tm-30) REVERT: A 226 VAL cc_start: 0.7865 (m) cc_final: 0.7626 (t) REVERT: A 246 LYS cc_start: 0.8601 (ptpt) cc_final: 0.8345 (ptpt) REVERT: A 272 MET cc_start: 0.8124 (tmm) cc_final: 0.7836 (tmm) REVERT: A 282 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7400 (mm-30) REVERT: A 386 ASP cc_start: 0.7496 (m-30) cc_final: 0.7137 (m-30) REVERT: A 393 MET cc_start: 0.8547 (mtp) cc_final: 0.8143 (mtp) REVERT: A 423 ASP cc_start: 0.8067 (m-30) cc_final: 0.7786 (m-30) REVERT: A 474 ASP cc_start: 0.7499 (m-30) cc_final: 0.7240 (m-30) REVERT: A 480 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6912 (tm-30) REVERT: A 566 LYS cc_start: 0.8308 (ttpp) cc_final: 0.8073 (ttpt) REVERT: B 32 ASN cc_start: 0.7953 (t0) cc_final: 0.7279 (t0) REVERT: B 95 LEU cc_start: 0.8590 (mm) cc_final: 0.8206 (mp) REVERT: B 136 LYS cc_start: 0.7819 (tptt) cc_final: 0.7150 (tptt) outliers start: 8 outliers final: 7 residues processed: 219 average time/residue: 0.0898 time to fit residues: 24.7708 Evaluate side-chains 222 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 215 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 341 THR Chi-restraints excluded: chain A residue 505 LYS 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: 0.7980 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 49 optimal weight: 0.0030 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.111824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.098989 restraints weight = 9760.032| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.64 r_work: 0.3111 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6367 Z= 0.178 Angle : 0.604 8.857 8647 Z= 0.305 Chirality : 0.043 0.160 970 Planarity : 0.004 0.043 1090 Dihedral : 10.601 138.522 926 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.54 % Allowed : 15.87 % Favored : 81.59 % 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 are not related in a simple way. whole: -0.02 (0.31), residues: 769 helix: 1.11 (0.31), residues: 296 sheet: 0.33 (0.45), residues: 151 loop : -1.25 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 77 TYR 0.012 0.001 TYR A 329 PHE 0.012 0.001 PHE A 433 TRP 0.011 0.001 TRP A 406 HIS 0.005 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 6367) covalent geometry : angle 0.60425 / 0.31 ( 8647) hydrogen bonds : bond 0.04929 / 3.25 ( 266) hydrogen bonds : angle 4.53522 / 3.11 ( 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 237 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 0.137 Fit side-chains REVERT: A 109 CYS cc_start: 0.7869 (m) cc_final: 0.7473 (m) REVERT: A 128 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7082 (tm-30) REVERT: A 226 VAL cc_start: 0.7854 (m) cc_final: 0.7401 (t) REVERT: A 246 LYS cc_start: 0.8623 (ptpt) cc_final: 0.8359 (ptpt) REVERT: A 316 MET cc_start: 0.8521 (mtt) cc_final: 0.8304 (mtt) REVERT: A 357 GLN cc_start: 0.8229 (mt0) cc_final: 0.7972 (mt0) REVERT: A 393 MET cc_start: 0.8560 (mtp) cc_final: 0.8154 (mtp) REVERT: A 423 ASP cc_start: 0.8059 (m-30) cc_final: 0.7769 (m-30) REVERT: A 463 LEU cc_start: 0.8477 (pp) cc_final: 0.8257 (pt) REVERT: A 464 GLU cc_start: 0.7535 (pm20) cc_final: 0.7161 (mp0) REVERT: A 474 ASP cc_start: 0.7513 (m-30) cc_final: 0.7259 (m-30) REVERT: A 480 GLU cc_start: 0.7350 (tm-30) cc_final: 0.6934 (tm-30) REVERT: A 566 LYS cc_start: 0.8264 (ttpp) cc_final: 0.8029 (ttpt) REVERT: A 598 ASP cc_start: 0.7487 (m-30) cc_final: 0.7280 (m-30) REVERT: B 32 ASN cc_start: 0.7894 (t0) cc_final: 0.7245 (t0) REVERT: B 95 LEU cc_start: 0.8621 (mm) cc_final: 0.8231 (mp) REVERT: B 136 LYS cc_start: 0.7756 (tptt) cc_final: 0.7291 (tptt) outliers start: 17 outliers final: 12 residues processed: 225 average time/residue: 0.0779 time to fit residues: 22.2092 Evaluate side-chains 228 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 216 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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 255 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 311 SER 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: 0.2980 chunk 42 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 0.0050 chunk 76 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 52 optimal weight: 0.7980 overall best weight: 0.3572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.113354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.100342 restraints weight = 9739.474| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.66 r_work: 0.3129 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1319 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= 0.126 Angle : 0.581 9.210 8647 Z= 0.290 Chirality : 0.042 0.157 970 Planarity : 0.004 0.042 1090 Dihedral : 10.576 138.033 926 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.40 % Allowed : 18.26 % Favored : 79.34 % 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 are not related in a simple way. whole: 0.10 (0.31), residues: 769 helix: 1.31 (0.31), residues: 292 sheet: 0.34 (0.45), residues: 149 loop : -1.22 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 77 TYR 0.013 0.001 TYR A 41 PHE 0.011 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/Z covalent geometry : bond 0.00283 / 0.13 ( 6367) covalent geometry : angle 0.58092 / 0.29 ( 8647) hydrogen bonds : bond 0.04294 / 2.83 ( 266) hydrogen bonds : angle 4.33937 / 2.99 ( 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 228 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 0.155 Fit side-chains REVERT: A 109 CYS cc_start: 0.7855 (m) cc_final: 0.7443 (m) REVERT: A 128 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7093 (tm-30) REVERT: A 235 PHE cc_start: 0.8388 (t80) cc_final: 0.8084 (t80) REVERT: A 246 LYS cc_start: 0.8603 (ptpt) cc_final: 0.8367 (ptpt) REVERT: A 272 MET cc_start: 0.8134 (tmm) cc_final: 0.7838 (tmm) REVERT: A 316 MET cc_start: 0.8501 (mtt) cc_final: 0.8299 (mtt) REVERT: A 357 GLN cc_start: 0.8208 (mt0) cc_final: 0.7992 (mt0) REVERT: A 377 ARG cc_start: 0.7693 (mmm160) cc_final: 0.7389 (mmm160) REVERT: A 393 MET cc_start: 0.8571 (mtp) cc_final: 0.8145 (mtp) REVERT: A 423 ASP cc_start: 0.8040 (m-30) cc_final: 0.7757 (m-30) REVERT: A 464 GLU cc_start: 0.7517 (pm20) cc_final: 0.7284 (mp0) REVERT: A 480 GLU cc_start: 0.7350 (tm-30) cc_final: 0.6958 (tm-30) REVERT: A 598 ASP cc_start: 0.7433 (m-30) cc_final: 0.7225 (m-30) REVERT: B 32 ASN cc_start: 0.7772 (t0) cc_final: 0.7123 (t0) REVERT: B 136 LYS cc_start: 0.7713 (tptt) cc_final: 0.7122 (tptt) outliers start: 16 outliers final: 13 residues processed: 217 average time/residue: 0.0764 time to fit residues: 21.0302 Evaluate side-chains 221 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 208 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 255 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 427 LEU 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: 3.9990 chunk 58 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.111016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.098218 restraints weight = 9957.454| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.66 r_work: 0.3094 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6367 Z= 0.206 Angle : 0.610 9.134 8647 Z= 0.309 Chirality : 0.044 0.154 970 Planarity : 0.004 0.042 1090 Dihedral : 10.479 135.500 926 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.40 % Allowed : 19.91 % 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 are not related in a simple way. whole: -0.01 (0.31), residues: 769 helix: 1.13 (0.31), residues: 296 sheet: 0.26 (0.45), residues: 151 loop : -1.20 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 369 TYR 0.015 0.002 TYR A 329 PHE 0.013 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/Z covalent geometry : bond 0.00474 / 0.21 ( 6367) covalent geometry : angle 0.60996 / 0.31 ( 8647) hydrogen bonds : bond 0.05021 / 3.35 ( 266) hydrogen bonds : angle 4.39989 / 3.04 ( 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 235 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 219 time to evaluate : 0.134 Fit side-chains REVERT: A 21 LEU cc_start: 0.8696 (mt) cc_final: 0.8382 (mp) REVERT: A 56 SER cc_start: 0.8666 (p) cc_final: 0.8343 (t) REVERT: A 65 ASP cc_start: 0.7799 (t0) cc_final: 0.7563 (t0) REVERT: A 109 CYS cc_start: 0.7920 (m) cc_final: 0.7499 (m) REVERT: A 121 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7503 (tp30) REVERT: A 128 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7199 (tm-30) REVERT: A 246 LYS cc_start: 0.8630 (ptpt) cc_final: 0.8368 (ptpt) REVERT: A 272 MET cc_start: 0.8142 (tmm) cc_final: 0.7870 (tmm) REVERT: A 357 GLN cc_start: 0.8257 (mt0) cc_final: 0.8013 (mt0) REVERT: A 377 ARG cc_start: 0.7708 (mmm160) cc_final: 0.7391 (mmm160) REVERT: A 393 MET cc_start: 0.8602 (mtp) cc_final: 0.8166 (mtp) REVERT: A 423 ASP cc_start: 0.8076 (m-30) cc_final: 0.7774 (m-30) REVERT: A 480 GLU cc_start: 0.7398 (tm-30) cc_final: 0.7081 (tm-30) REVERT: A 566 LYS cc_start: 0.8264 (ttpp) cc_final: 0.8025 (ttpt) REVERT: B 32 ASN cc_start: 0.7951 (t0) cc_final: 0.7283 (t0) REVERT: B 136 LYS cc_start: 0.7753 (tptt) cc_final: 0.7162 (tptt) outliers start: 16 outliers final: 12 residues processed: 224 average time/residue: 0.0762 time to fit residues: 21.4449 Evaluate side-chains 229 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 217 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 255 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 52 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 63 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.112010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.099274 restraints weight = 9853.314| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.69 r_work: 0.3121 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1466 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= 0.150 Angle : 0.589 10.055 8647 Z= 0.297 Chirality : 0.042 0.174 970 Planarity : 0.004 0.040 1090 Dihedral : 10.492 135.243 926 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.25 % Allowed : 20.96 % Favored : 76.80 % 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 are not related in a simple way. whole: 0.14 (0.31), residues: 769 helix: 1.36 (0.31), residues: 290 sheet: 0.29 (0.45), residues: 151 loop : -1.15 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 77 TYR 0.013 0.001 TYR A 329 PHE 0.011 0.001 PHE A 433 TRP 0.012 0.001 TRP A 406 HIS 0.002 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 6367) covalent geometry : angle 0.58949 / 0.30 ( 8647) hydrogen bonds : bond 0.04527 / 3.00 ( 266) hydrogen bonds : angle 4.30127 / 2.97 ( 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 230 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 215 time to evaluate : 0.174 Fit side-chains REVERT: A 56 SER cc_start: 0.8671 (p) cc_final: 0.8335 (t) REVERT: A 109 CYS cc_start: 0.7993 (m) cc_final: 0.7577 (m) REVERT: A 121 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7494 (tp30) REVERT: A 128 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7207 (tm-30) REVERT: A 246 LYS cc_start: 0.8623 (ptpt) cc_final: 0.8355 (ptpt) REVERT: A 272 MET cc_start: 0.8153 (tmm) cc_final: 0.7897 (tmm) REVERT: A 357 GLN cc_start: 0.8258 (mt0) cc_final: 0.8018 (mt0) REVERT: A 377 ARG cc_start: 0.7715 (mmm160) cc_final: 0.7396 (mmm160) REVERT: A 393 MET cc_start: 0.8567 (mtp) cc_final: 0.8134 (mtp) REVERT: A 423 ASP cc_start: 0.8065 (m-30) cc_final: 0.7784 (m-30) REVERT: A 474 ASP cc_start: 0.7596 (m-30) cc_final: 0.7350 (m-30) REVERT: A 480 GLU cc_start: 0.7400 (tm-30) cc_final: 0.7071 (tm-30) REVERT: B 32 ASN cc_start: 0.7805 (t0) cc_final: 0.7344 (t0) REVERT: B 136 LYS cc_start: 0.7727 (tptt) cc_final: 0.7116 (tptt) outliers start: 15 outliers final: 14 residues processed: 218 average time/residue: 0.0686 time to fit residues: 18.7814 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 : 0.158 ------------------------------------------------------------------------------- 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 255 LEU Chi-restraints excluded: chain A residue 256 LEU 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 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: 1.9990 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 67 optimal weight: 0.0570 chunk 49 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 26 optimal weight: 0.0980 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.112666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.100004 restraints weight = 9864.019| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.68 r_work: 0.3125 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1553 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= 0.124 Angle : 0.589 10.710 8647 Z= 0.296 Chirality : 0.042 0.186 970 Planarity : 0.004 0.039 1090 Dihedral : 10.514 135.126 926 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.54 % Allowed : 22.16 % 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 are not related in a simple way. whole: 0.16 (0.31), residues: 769 helix: 1.37 (0.31), residues: 292 sheet: 0.30 (0.45), residues: 151 loop : -1.15 (0.34), residues: 326 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/Z covalent geometry : bond 0.00275 / 0.12 ( 6367) covalent geometry : angle 0.58926 / 0.30 ( 8647) hydrogen bonds : bond 0.04300 / 2.80 ( 266) hydrogen bonds : angle 4.25940 / 2.95 ( 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 225 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.155 Fit side-chains REVERT: A 29 HIS cc_start: 0.6273 (t70) cc_final: 0.6045 (t70) REVERT: A 56 SER cc_start: 0.8669 (p) cc_final: 0.8333 (t) REVERT: A 109 CYS cc_start: 0.8006 (m) cc_final: 0.7586 (m) REVERT: A 121 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7479 (tp30) REVERT: A 128 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7215 (tm-30) REVERT: A 246 LYS cc_start: 0.8631 (ptpt) cc_final: 0.8356 (ptpt) REVERT: A 272 MET cc_start: 0.8149 (tmm) cc_final: 0.7889 (tmm) REVERT: A 316 MET cc_start: 0.8496 (mtt) cc_final: 0.8247 (mtt) REVERT: A 357 GLN cc_start: 0.8235 (mt0) cc_final: 0.8014 (mt0) REVERT: A 377 ARG cc_start: 0.7679 (mmm160) cc_final: 0.7342 (mmm160) REVERT: A 393 MET cc_start: 0.8546 (mtp) cc_final: 0.8108 (mtp) REVERT: A 423 ASP cc_start: 0.8056 (m-30) cc_final: 0.7775 (m-30) REVERT: A 474 ASP cc_start: 0.7596 (m-30) cc_final: 0.7340 (m-30) REVERT: A 480 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7082 (tm-30) REVERT: B 32 ASN cc_start: 0.7720 (t0) cc_final: 0.7050 (t0) REVERT: B 136 LYS cc_start: 0.7703 (tptt) cc_final: 0.7109 (tptt) outliers start: 17 outliers final: 16 residues processed: 212 average time/residue: 0.0731 time to fit residues: 19.5505 Evaluate side-chains 224 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 96 LEU Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 255 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 341 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 47 optimal weight: 0.0970 chunk 22 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 overall best weight: 0.1916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.101136 restraints weight = 9884.472| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.69 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: 0.8123 moved from start: 0.1724 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= 0.107 Angle : 0.585 10.900 8647 Z= 0.294 Chirality : 0.041 0.185 970 Planarity : 0.004 0.038 1090 Dihedral : 10.428 135.511 926 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.54 % Allowed : 21.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.31), residues: 769 helix: 1.38 (0.31), residues: 292 sheet: 0.42 (0.47), residues: 141 loop : -1.06 (0.34), residues: 336 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 0.009 0.001 PHE A 127 TRP 0.008 0.001 TRP A 458 HIS 0.002 0.000 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 6367) covalent geometry : angle 0.58544 / 0.29 ( 8647) hydrogen bonds : bond 0.03830 / 2.50 ( 266) hydrogen bonds : angle 4.16454 / 2.88 ( 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 218 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 0.214 Fit side-chains REVERT: A 29 HIS cc_start: 0.6223 (t70) cc_final: 0.6004 (t70) REVERT: A 56 SER cc_start: 0.8650 (p) cc_final: 0.8324 (t) REVERT: A 65 ASP cc_start: 0.7768 (t0) cc_final: 0.7520 (t0) REVERT: A 128 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7200 (tm-30) REVERT: A 246 LYS cc_start: 0.8634 (ptpt) cc_final: 0.8360 (ptpt) REVERT: A 272 MET cc_start: 0.8093 (tmm) cc_final: 0.7829 (tmm) REVERT: A 393 MET cc_start: 0.8555 (mtp) cc_final: 0.8129 (mtp) REVERT: A 423 ASP cc_start: 0.8021 (m-30) cc_final: 0.7749 (m-30) REVERT: A 480 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7093 (tm-30) REVERT: B 32 ASN cc_start: 0.7819 (t0) cc_final: 0.7168 (t0) REVERT: B 136 LYS cc_start: 0.7602 (tptt) cc_final: 0.7030 (tptt) outliers start: 17 outliers final: 14 residues processed: 207 average time/residue: 0.0730 time to fit residues: 19.1633 Evaluate side-chains 212 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 255 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 54 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 45 optimal weight: 0.0770 chunk 55 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3451 r_free = 0.3451 target = 0.112026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.099177 restraints weight = 9903.861| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.68 r_work: 0.3111 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6367 Z= 0.156 Angle : 0.594 11.208 8647 Z= 0.300 Chirality : 0.042 0.186 970 Planarity : 0.004 0.039 1090 Dihedral : 10.374 134.478 926 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.80 % Allowed : 23.35 % Favored : 74.85 % 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 are not related in a simple way. whole: 0.22 (0.31), residues: 769 helix: 1.39 (0.31), residues: 292 sheet: 0.39 (0.47), residues: 141 loop : -1.07 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 46 TYR 0.014 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/Z covalent geometry : bond 0.00355 / 0.16 ( 6367) covalent geometry : angle 0.59432 / 0.30 ( 8647) hydrogen bonds : bond 0.04378 / 2.88 ( 266) hydrogen bonds : angle 4.22016 / 2.92 ( 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 221 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 209 time to evaluate : 0.219 Fit side-chains REVERT: A 29 HIS cc_start: 0.6285 (t70) cc_final: 0.6056 (t70) REVERT: A 56 SER cc_start: 0.8652 (p) cc_final: 0.8328 (t) REVERT: A 65 ASP cc_start: 0.7782 (t0) cc_final: 0.7563 (t0) REVERT: A 109 CYS cc_start: 0.7956 (m) cc_final: 0.7528 (m) REVERT: A 128 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7215 (tm-30) REVERT: A 246 LYS cc_start: 0.8639 (ptpt) cc_final: 0.8374 (ptpt) REVERT: A 272 MET cc_start: 0.8119 (tmm) cc_final: 0.7852 (tmm) REVERT: A 377 ARG cc_start: 0.7723 (mmm160) cc_final: 0.7382 (mmm160) REVERT: A 393 MET cc_start: 0.8602 (mtp) cc_final: 0.8149 (mtp) REVERT: A 474 ASP cc_start: 0.7576 (m-30) cc_final: 0.7330 (m-30) REVERT: A 480 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7106 (tm-30) REVERT: B 32 ASN cc_start: 0.7818 (t0) cc_final: 0.7126 (t0) REVERT: B 136 LYS cc_start: 0.7651 (tptt) cc_final: 0.7063 (tptt) REVERT: B 141 LEU cc_start: 0.8645 (mm) cc_final: 0.8308 (mt) outliers start: 12 outliers final: 12 residues processed: 213 average time/residue: 0.0775 time to fit residues: 20.7964 Evaluate side-chains 220 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 255 LEU 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 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=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: 0.9990 chunk 15 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3438 r_free = 0.3438 target = 0.111060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.098316 restraints weight = 9874.344| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.66 r_work: 0.3092 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6367 Z= 0.208 Angle : 0.643 11.230 8647 Z= 0.327 Chirality : 0.044 0.191 970 Planarity : 0.004 0.041 1090 Dihedral : 10.326 133.172 926 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.10 % Allowed : 23.05 % Favored : 74.85 % 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 are not related in a simple way. whole: 0.12 (0.31), residues: 769 helix: 1.30 (0.31), residues: 290 sheet: 0.38 (0.47), residues: 141 loop : -1.13 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 369 TYR 0.015 0.001 TYR A 329 PHE 0.013 0.002 PHE A 452 TRP 0.009 0.001 TRP A 406 HIS 0.003 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 ( 6367) covalent geometry : angle 0.64291 / 0.33 ( 8647) hydrogen bonds : bond 0.04944 / 3.28 ( 266) hydrogen bonds : angle 4.35643 / 3.02 ( 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 229 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 215 time to evaluate : 0.132 Fit side-chains REVERT: A 56 SER cc_start: 0.8671 (p) cc_final: 0.8349 (t) REVERT: A 65 ASP cc_start: 0.7782 (t0) cc_final: 0.7566 (t0) REVERT: A 109 CYS cc_start: 0.7942 (m) cc_final: 0.7517 (m) REVERT: A 121 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7473 (tp30) REVERT: A 128 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7236 (tm-30) REVERT: A 246 LYS cc_start: 0.8640 (ptpt) cc_final: 0.8352 (ptpt) REVERT: A 272 MET cc_start: 0.8137 (tmm) cc_final: 0.7883 (tmm) REVERT: A 377 ARG cc_start: 0.7715 (mmm160) cc_final: 0.7381 (mmm160) REVERT: A 393 MET cc_start: 0.8600 (mtp) cc_final: 0.8147 (mtp) REVERT: A 423 ASP cc_start: 0.8068 (m-30) cc_final: 0.7783 (m-30) REVERT: A 474 ASP cc_start: 0.7527 (m-30) cc_final: 0.7266 (m-30) REVERT: A 480 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7122 (tm-30) REVERT: A 567 GLN cc_start: 0.8204 (tp40) cc_final: 0.7927 (tp40) REVERT: B 32 ASN cc_start: 0.7819 (t0) cc_final: 0.7117 (t0) REVERT: B 136 LYS cc_start: 0.7671 (tptt) cc_final: 0.7078 (tptt) REVERT: B 141 LEU cc_start: 0.8661 (mm) cc_final: 0.8315 (mt) outliers start: 14 outliers final: 13 residues processed: 219 average time/residue: 0.0768 time to fit residues: 21.2300 Evaluate side-chains 226 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 213 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 144 GLU Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 255 LEU 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 556 VAL 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: 0.9980 chunk 50 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 60 optimal weight: 0.0270 chunk 62 optimal weight: 0.0020 chunk 49 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.0060 overall best weight: 0.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3469 r_free = 0.3469 target = 0.113086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.100427 restraints weight = 9828.711| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.64 r_work: 0.3138 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1755 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= 0.116 Angle : 0.597 11.614 8647 Z= 0.302 Chirality : 0.041 0.203 970 Planarity : 0.004 0.037 1090 Dihedral : 10.403 133.773 926 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.35 % Allowed : 23.95 % Favored : 74.70 % 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 are not related in a simple way. whole: 0.20 (0.31), residues: 769 helix: 1.35 (0.31), residues: 292 sheet: 0.43 (0.46), residues: 143 loop : -1.12 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 369 TYR 0.017 0.001 TYR A 329 PHE 0.010 0.001 PHE A 433 TRP 0.009 0.001 TRP A 458 HIS 0.002 0.000 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 6367) covalent geometry : angle 0.59727 / 0.30 ( 8647) hydrogen bonds : bond 0.04070 / 2.68 ( 266) hydrogen bonds : angle 4.22609 / 2.93 ( 786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1202.53 seconds wall clock time: 21 minutes 14.83 seconds (1274.83 seconds total)