Starting phenix.real_space_refine on Thu Jul 2 07:30:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dc2_27320/07_2026/8dc2_27320.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dc2_27320/07_2026/8dc2_27320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dc2_27320/07_2026/8dc2_27320.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dc2_27320/07_2026/8dc2_27320.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dc2_27320/07_2026/8dc2_27320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dc2_27320/07_2026/8dc2_27320.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dc2_27320/07_2026/8dc2_27320.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dc2_27320/07_2026/8dc2_27320.cif" } resolution = 2.99 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= 0.179 sd= 1.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 132 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 86 5.49 5 S 32 5.16 5 C 4326 2.51 5 N 1221 2.21 5 O 1631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7296 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5483 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 10, 'TRANS': 662} Chain breaks: 2 Chain: "B" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1069 Classifications: {'RNA': 51} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 18, 'rna3p_pyr': 25} Link IDs: {'rna2p': 8, 'rna3p': 42} Chain: "C" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 542 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "D" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Time building chain proxies: 1.44, per 1000 atoms: 0.20 Number of scatterers: 7296 At special positions: 0 Unit cell: (80.28, 92.545, 110.385, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 86 15.00 O 1631 8.00 N 1221 7.00 C 4326 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: 0.47 Conformation dependent library (CDL) restraints added in 265.3 milliseconds 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1286 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 3 sheets defined 57.1% alpha, 10.5% beta 33 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 27 through 52 Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 71 through 79 removed outlier: 3.607A pdb=" N THR A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 96 through 112 Processing helix chain 'A' and resid 124 through 131 Processing helix chain 'A' and resid 132 through 146 Processing helix chain 'A' and resid 162 through 177 removed outlier: 4.302A pdb=" N ASN A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 195 Processing helix chain 'A' and resid 199 through 215 removed outlier: 4.049A pdb=" N ARG A 205 " --> pdb=" O ASN A 201 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 234 removed outlier: 3.944A pdb=" N LYS A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.707A pdb=" N LYS A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 386 Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'A' and resid 413 through 435 removed outlier: 3.530A pdb=" N LYS A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 472 removed outlier: 3.882A pdb=" N ARG A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'A' and resid 483 through 486 Processing helix chain 'A' and resid 487 through 523 removed outlier: 3.501A pdb=" N GLY A 523 " --> pdb=" O PHE A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 611 removed outlier: 3.639A pdb=" N ILE A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 627 removed outlier: 4.280A pdb=" N ASN A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.786A pdb=" N VAL A 668 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A 669 " --> pdb=" O HIS A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 669' Processing helix chain 'A' and resid 680 through 695 removed outlier: 3.842A pdb=" N MET A 693 " --> pdb=" O ILE A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 702 Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.567A pdb=" N LYS A 733 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU A 735 " --> pdb=" O LYS A 731 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 246 through 250 removed outlier: 5.878A pdb=" N ASN A 317 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER A 302 " --> pdb=" O ASP A 315 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASP A 315 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL A 304 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TYR A 313 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS A 306 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLU A 311 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE A 312 " --> pdb=" O ILE A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AA3, first strand: chain 'A' and resid 388 through 391 removed outlier: 5.267A pdb=" N ILE A 348 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N PHE A 391 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N THR A 346 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY A 334 " --> pdb=" O ASN A 347 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N LEU A 349 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 13.098A pdb=" N VAL A 332 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 333 " --> pdb=" O SER A 528 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLU A 530 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N ILE A 335 " --> pdb=" O GLU A 530 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL A 527 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL A 634 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 529 " --> pdb=" O VAL A 634 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR A 718 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 720 " --> pdb=" O LEU A 633 " (cutoff:3.500A) 293 hydrogen bonds defined for protein. 834 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 166 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1697 1.33 - 1.45: 2004 1.45 - 1.57: 3690 1.57 - 1.69: 170 1.69 - 1.81: 56 Bond restraints: 7617 Sorted by residual: bond pdb=" C3' DT C -2 " pdb=" C2' DT C -2 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.24e+00 bond pdb=" C3' DG C -9 " pdb=" C2' DG C -9 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.69e+00 bond pdb=" C3' DA C 2 " pdb=" C2' DA C 2 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.08e+00 bond pdb=" C3' DT D -1 " pdb=" C2' DT D -1 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.89e+00 bond pdb=" C3' DT C -5 " pdb=" C2' DT C -5 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.84e+00 ... (remaining 7612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 10083 1.18 - 2.36: 465 2.36 - 3.54: 87 3.54 - 4.72: 17 4.72 - 5.90: 5 Bond angle restraints: 10657 Sorted by residual: angle pdb=" N3 DT C -8 " pdb=" C4 DT C -8 " pdb=" O4 DT C -8 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT D -2 " pdb=" C4 DT D -2 " pdb=" O4 DT D -2 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT C -14 " pdb=" C4 DT C -14 " pdb=" O4 DT C -14 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT D -1 " pdb=" C4 DT D -1 " pdb=" O4 DT D -1 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT C -2 " pdb=" C4 DT C -2 " pdb=" O4 DT C -2 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 10652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.63: 4155 34.63 - 69.26: 206 69.26 - 103.89: 8 103.89 - 138.52: 1 138.52 - 173.15: 3 Dihedral angle restraints: 4373 sinusoidal: 2376 harmonic: 1997 Sorted by residual: dihedral pdb=" O4' U B 1 " pdb=" C1' U B 1 " pdb=" N1 U B 1 " pdb=" C2 U B 1 " ideal model delta sinusoidal sigma weight residual 232.00 58.85 173.15 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" CA MET A 607 " pdb=" C MET A 607 " pdb=" N ILE A 608 " pdb=" CA ILE A 608 " ideal model delta harmonic sigma weight residual 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ILE A 157 " pdb=" C ILE A 157 " pdb=" N SER A 158 " pdb=" CA SER A 158 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 4370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 822 0.034 - 0.069: 281 0.069 - 0.103: 82 0.103 - 0.138: 27 0.138 - 0.172: 2 Chirality restraints: 1214 Sorted by residual: chirality pdb=" C3' U B -12 " pdb=" C4' U B -12 " pdb=" O3' U B -12 " pdb=" C2' U B -12 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" C3' DG D -8 " pdb=" C4' DG D -8 " pdb=" O3' DG D -8 " pdb=" C2' DG D -8 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CB THR A 165 " pdb=" CA THR A 165 " pdb=" OG1 THR A 165 " pdb=" CG2 THR A 165 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 1211 not shown) Planarity restraints: 1042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG C -15 " 0.014 2.00e-02 2.50e+03 9.92e-03 2.95e+00 pdb=" N9 DG C -15 " -0.011 2.00e-02 2.50e+03 pdb=" C8 DG C -15 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG C -15 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG C -15 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG C -15 " -0.006 2.00e-02 2.50e+03 pdb=" O6 DG C -15 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DG C -15 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG C -15 " -0.024 2.00e-02 2.50e+03 pdb=" N2 DG C -15 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DG C -15 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG C -15 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 126 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C THR A 126 " -0.028 2.00e-02 2.50e+03 pdb=" O THR A 126 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR A 127 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B -3 " -0.019 2.00e-02 2.50e+03 1.07e-02 2.57e+00 pdb=" N1 C B -3 " 0.025 2.00e-02 2.50e+03 pdb=" C2 C B -3 " 0.003 2.00e-02 2.50e+03 pdb=" O2 C B -3 " -0.001 2.00e-02 2.50e+03 pdb=" N3 C B -3 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C B -3 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C B -3 " -0.003 2.00e-02 2.50e+03 pdb=" C5 C B -3 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C B -3 " 0.003 2.00e-02 2.50e+03 ... (remaining 1039 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 979 2.75 - 3.29: 7349 3.29 - 3.83: 13416 3.83 - 4.36: 15837 4.36 - 4.90: 24413 Nonbonded interactions: 61994 Sorted by model distance: nonbonded pdb=" OH TYR A 42 " pdb=" OD1 ASN A 140 " model vdw 2.216 3.040 nonbonded pdb=" NZ LYS A 155 " pdb=" O SER A 158 " model vdw 2.217 3.120 nonbonded pdb=" NE2 HIS A 612 " pdb=" OP1 DT C -8 " model vdw 2.289 3.120 nonbonded pdb=" O LEU A 121 " pdb=" ND2 ASN A 274 " model vdw 2.292 3.120 nonbonded pdb=" O2' U B -19 " pdb=" OP1 U B -16 " model vdw 2.301 3.040 ... (remaining 61989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.820 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 : 0.004 0.042 7617 Z= 0.262 Angle : 0.586 5.898 10657 Z= 0.404 Chirality : 0.040 0.172 1214 Planarity : 0.003 0.029 1042 Dihedral : 17.760 173.155 3087 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.68 % 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: 1.17 (0.33), residues: 667 helix: 1.96 (0.30), residues: 327 sheet: 0.43 (0.60), residues: 71 loop : -0.60 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.017 0.001 TYR A 133 PHE 0.017 0.001 PHE A 400 TRP 0.006 0.001 TRP A 429 HIS 0.005 0.001 HIS A 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.26 ( 7617) covalent geometry : angle 0.58574 / 0.40 (10657) hydrogen bonds : bond 0.14088 / 9.50 ( 376) hydrogen bonds : angle 5.55034 / 3.69 ( 1000) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.225 Fit side-chains REVERT: A 90 MET cc_start: 0.7248 (mtm) cc_final: 0.6849 (mtm) REVERT: A 174 MET cc_start: 0.6426 (mmp) cc_final: 0.6132 (mmt) REVERT: A 230 ASP cc_start: 0.7729 (t0) cc_final: 0.7518 (t0) REVERT: A 288 ASP cc_start: 0.7563 (t70) cc_final: 0.7332 (t70) REVERT: A 488 ASP cc_start: 0.8276 (p0) cc_final: 0.7965 (p0) REVERT: A 695 ASN cc_start: 0.7883 (OUTLIER) cc_final: 0.7545 (t0) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.3854 time to fit residues: 55.1317 Evaluate side-chains 104 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 ASN A 140 ASN A 176 HIS A 265 ASN A 413 ASN A 522 ASN A 605 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.090015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.076876 restraints weight = 15771.397| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.86 r_work: 0.3035 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7617 Z= 0.253 Angle : 0.646 6.596 10657 Z= 0.355 Chirality : 0.043 0.257 1214 Planarity : 0.004 0.030 1042 Dihedral : 19.165 173.574 1727 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.74 % Allowed : 9.82 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.98 (0.33), residues: 667 helix: 1.71 (0.29), residues: 334 sheet: 0.17 (0.58), residues: 71 loop : -0.57 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 240 TYR 0.021 0.002 TYR A 133 PHE 0.014 0.002 PHE A 613 TRP 0.023 0.003 TRP A 185 HIS 0.007 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.25 ( 7617) covalent geometry : angle 0.64631 / 0.36 (10657) hydrogen bonds : bond 0.05484 / 3.68 ( 376) hydrogen bonds : angle 4.72129 / 3.17 ( 1000) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8625 (tp30) cc_final: 0.8366 (tp30) REVERT: A 206 MET cc_start: 0.8056 (mmm) cc_final: 0.7498 (mmt) REVERT: A 230 ASP cc_start: 0.8438 (t0) cc_final: 0.8028 (t0) REVERT: A 233 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8095 (pp) REVERT: A 288 ASP cc_start: 0.8509 (t70) cc_final: 0.8276 (t70) REVERT: A 363 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: A 488 ASP cc_start: 0.8526 (p0) cc_final: 0.8000 (p0) REVERT: A 680 ASN cc_start: 0.8538 (t0) cc_final: 0.8328 (t0) REVERT: A 704 LYS cc_start: 0.6988 (OUTLIER) cc_final: 0.5626 (ttmt) outliers start: 17 outliers final: 5 residues processed: 113 average time/residue: 0.4229 time to fit residues: 51.0934 Evaluate side-chains 103 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 53 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 ASN ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.091120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.077841 restraints weight = 15660.768| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.86 r_work: 0.3057 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7617 Z= 0.185 Angle : 0.591 6.627 10657 Z= 0.331 Chirality : 0.042 0.264 1214 Planarity : 0.003 0.027 1042 Dihedral : 19.056 173.214 1725 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.22 % Allowed : 13.04 % Favored : 83.74 % 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: 0.95 (0.33), residues: 667 helix: 1.69 (0.29), residues: 333 sheet: 0.11 (0.59), residues: 71 loop : -0.55 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 240 TYR 0.020 0.002 TYR A 133 PHE 0.014 0.002 PHE A 400 TRP 0.013 0.002 TRP A 185 HIS 0.003 0.001 HIS A 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 ( 7617) covalent geometry : angle 0.59074 / 0.33 (10657) hydrogen bonds : bond 0.04782 / 3.18 ( 376) hydrogen bonds : angle 4.54032 / 3.04 ( 1000) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8571 (tp30) cc_final: 0.8191 (tp30) REVERT: A 206 MET cc_start: 0.8085 (mmm) cc_final: 0.7534 (mmt) REVERT: A 230 ASP cc_start: 0.8418 (t0) cc_final: 0.7982 (t0) REVERT: A 233 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8035 (pp) REVERT: A 288 ASP cc_start: 0.8524 (t70) cc_final: 0.8270 (t70) REVERT: A 363 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7694 (mt-10) REVERT: A 488 ASP cc_start: 0.8453 (p0) cc_final: 0.7937 (p0) REVERT: A 502 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8858 (mtmm) REVERT: A 680 ASN cc_start: 0.8418 (t0) cc_final: 0.8167 (t0) outliers start: 20 outliers final: 7 residues processed: 113 average time/residue: 0.3989 time to fit residues: 48.2014 Evaluate side-chains 106 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 0.0670 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.5724 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.090294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.077035 restraints weight = 15915.689| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.90 r_work: 0.3040 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7617 Z= 0.204 Angle : 0.591 6.712 10657 Z= 0.329 Chirality : 0.042 0.256 1214 Planarity : 0.003 0.028 1042 Dihedral : 19.097 172.508 1725 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.58 % Allowed : 15.14 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.33), residues: 667 helix: 1.73 (0.29), residues: 340 sheet: -0.00 (0.59), residues: 71 loop : -0.58 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 699 TYR 0.023 0.002 TYR A 172 PHE 0.017 0.002 PHE A 604 TRP 0.012 0.002 TRP A 185 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 ( 7617) covalent geometry : angle 0.59072 / 0.33 (10657) hydrogen bonds : bond 0.04734 / 3.14 ( 376) hydrogen bonds : angle 4.50106 / 3.02 ( 1000) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.166 Fit side-chains REVERT: A 59 GLU cc_start: 0.8594 (tp30) cc_final: 0.8187 (tp30) REVERT: A 206 MET cc_start: 0.8110 (mmm) cc_final: 0.7615 (mmt) REVERT: A 230 ASP cc_start: 0.8408 (t0) cc_final: 0.7990 (t0) REVERT: A 233 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8048 (pp) REVERT: A 288 ASP cc_start: 0.8546 (t70) cc_final: 0.8282 (t70) REVERT: A 337 VAL cc_start: 0.8757 (t) cc_final: 0.8505 (p) REVERT: A 363 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: A 488 ASP cc_start: 0.8444 (p0) cc_final: 0.7914 (p0) REVERT: A 502 LYS cc_start: 0.9078 (mtmt) cc_final: 0.8862 (mtmm) REVERT: A 680 ASN cc_start: 0.8477 (t0) cc_final: 0.8231 (t0) outliers start: 16 outliers final: 8 residues processed: 112 average time/residue: 0.3871 time to fit residues: 46.5759 Evaluate side-chains 110 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 72 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 6 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 32 optimal weight: 0.0370 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 5 optimal weight: 0.0000 overall best weight: 0.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.092602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.079259 restraints weight = 15862.542| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.90 r_work: 0.3077 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7617 Z= 0.134 Angle : 0.562 9.826 10657 Z= 0.315 Chirality : 0.040 0.251 1214 Planarity : 0.003 0.028 1042 Dihedral : 19.035 173.467 1725 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.90 % Allowed : 15.78 % Favored : 81.32 % 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: 1.03 (0.33), residues: 667 helix: 1.76 (0.28), residues: 341 sheet: -0.00 (0.59), residues: 69 loop : -0.56 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 440 TYR 0.019 0.001 TYR A 133 PHE 0.016 0.001 PHE A 603 TRP 0.048 0.003 TRP A 185 HIS 0.003 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 7617) covalent geometry : angle 0.56235 / 0.31 (10657) hydrogen bonds : bond 0.04387 / 2.87 ( 376) hydrogen bonds : angle 4.37570 / 2.92 ( 1000) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8549 (tp30) cc_final: 0.8107 (tp30) REVERT: A 206 MET cc_start: 0.8102 (mmm) cc_final: 0.7596 (mmt) REVERT: A 230 ASP cc_start: 0.8397 (t0) cc_final: 0.7974 (t0) REVERT: A 233 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8021 (pp) REVERT: A 288 ASP cc_start: 0.8535 (t70) cc_final: 0.8258 (t70) REVERT: A 363 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7901 (mm-30) REVERT: A 488 ASP cc_start: 0.8414 (p0) cc_final: 0.7904 (p0) REVERT: A 502 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8825 (mtmm) REVERT: A 680 ASN cc_start: 0.8455 (t0) cc_final: 0.8216 (t0) outliers start: 18 outliers final: 8 residues processed: 115 average time/residue: 0.3598 time to fit residues: 44.4838 Evaluate side-chains 111 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 22 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 5 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 347 ASN A 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.091066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.077833 restraints weight = 15774.279| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.88 r_work: 0.3057 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7617 Z= 0.186 Angle : 0.583 7.692 10657 Z= 0.324 Chirality : 0.041 0.243 1214 Planarity : 0.003 0.028 1042 Dihedral : 19.065 173.021 1725 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.90 % Allowed : 17.39 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.99 (0.33), residues: 667 helix: 1.70 (0.28), residues: 343 sheet: -0.04 (0.59), residues: 69 loop : -0.54 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.020 0.002 TYR A 133 PHE 0.013 0.002 PHE A 396 TRP 0.033 0.003 TRP A 185 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 ( 7617) covalent geometry : angle 0.58267 / 0.32 (10657) hydrogen bonds : bond 0.04583 / 3.02 ( 376) hydrogen bonds : angle 4.44377 / 2.96 ( 1000) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8568 (tp30) cc_final: 0.8115 (tp30) REVERT: A 206 MET cc_start: 0.8126 (mmm) cc_final: 0.7704 (mmt) REVERT: A 230 ASP cc_start: 0.8457 (t0) cc_final: 0.8022 (t0) REVERT: A 233 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8019 (pp) REVERT: A 288 ASP cc_start: 0.8597 (t70) cc_final: 0.8306 (t70) REVERT: A 337 VAL cc_start: 0.8566 (t) cc_final: 0.8320 (p) REVERT: A 363 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7956 (mm-30) REVERT: A 488 ASP cc_start: 0.8486 (p0) cc_final: 0.7976 (p0) REVERT: A 502 LYS cc_start: 0.9052 (mtmt) cc_final: 0.8839 (mtmm) REVERT: A 680 ASN cc_start: 0.8476 (t0) cc_final: 0.8223 (t0) outliers start: 18 outliers final: 9 residues processed: 108 average time/residue: 0.3967 time to fit residues: 46.0245 Evaluate side-chains 105 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.091404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.078204 restraints weight = 15833.357| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.88 r_work: 0.3069 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 7617 Z= 0.173 Angle : 0.585 9.071 10657 Z= 0.324 Chirality : 0.041 0.242 1214 Planarity : 0.003 0.028 1042 Dihedral : 19.085 173.121 1725 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.74 % Allowed : 18.20 % Favored : 79.07 % 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: 0.99 (0.33), residues: 667 helix: 1.73 (0.28), residues: 341 sheet: -0.07 (0.59), residues: 69 loop : -0.55 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 440 TYR 0.025 0.002 TYR A 172 PHE 0.011 0.001 PHE A 396 TRP 0.024 0.003 TRP A 185 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 ( 7617) covalent geometry : angle 0.58465 / 0.32 (10657) hydrogen bonds : bond 0.04502 / 2.97 ( 376) hydrogen bonds : angle 4.39634 / 2.93 ( 1000) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8566 (tp30) cc_final: 0.8101 (tp30) REVERT: A 206 MET cc_start: 0.8109 (mmm) cc_final: 0.7677 (mmt) REVERT: A 230 ASP cc_start: 0.8401 (t0) cc_final: 0.7985 (t0) REVERT: A 233 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8022 (pp) REVERT: A 288 ASP cc_start: 0.8568 (t70) cc_final: 0.8276 (t70) REVERT: A 337 VAL cc_start: 0.8504 (t) cc_final: 0.8292 (p) REVERT: A 340 LYS cc_start: 0.8600 (tppp) cc_final: 0.8399 (tppp) REVERT: A 363 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7829 (mm-30) REVERT: A 400 PHE cc_start: 0.8557 (t80) cc_final: 0.8338 (t80) REVERT: A 488 ASP cc_start: 0.8434 (p0) cc_final: 0.7912 (p0) REVERT: A 502 LYS cc_start: 0.9048 (mtmt) cc_final: 0.8829 (mtmm) REVERT: A 680 ASN cc_start: 0.8454 (t0) cc_final: 0.8216 (t0) outliers start: 17 outliers final: 9 residues processed: 110 average time/residue: 0.3754 time to fit residues: 44.1771 Evaluate side-chains 108 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 0.0470 chunk 69 optimal weight: 5.9990 overall best weight: 1.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.089700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.076563 restraints weight = 15984.611| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.91 r_work: 0.3028 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 7617 Z= 0.229 Angle : 0.616 8.916 10657 Z= 0.340 Chirality : 0.043 0.240 1214 Planarity : 0.003 0.029 1042 Dihedral : 19.174 172.288 1725 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.22 % Allowed : 17.87 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.33), residues: 667 helix: 1.68 (0.29), residues: 335 sheet: -0.12 (0.61), residues: 67 loop : -0.60 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 440 TYR 0.025 0.002 TYR A 172 PHE 0.012 0.002 PHE A 599 TRP 0.022 0.003 TRP A 185 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.23 ( 7617) covalent geometry : angle 0.61614 / 0.34 (10657) hydrogen bonds : bond 0.04721 / 3.12 ( 376) hydrogen bonds : angle 4.46942 / 2.99 ( 1000) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8615 (tp30) cc_final: 0.8128 (tp30) REVERT: A 206 MET cc_start: 0.8130 (mmm) cc_final: 0.7689 (mmt) REVERT: A 230 ASP cc_start: 0.8480 (t0) cc_final: 0.8057 (t0) REVERT: A 233 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8095 (pp) REVERT: A 288 ASP cc_start: 0.8610 (t70) cc_final: 0.8314 (t70) REVERT: A 337 VAL cc_start: 0.8646 (t) cc_final: 0.8427 (p) REVERT: A 363 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7951 (mm-30) REVERT: A 488 ASP cc_start: 0.8523 (p0) cc_final: 0.8000 (p0) REVERT: A 502 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8845 (mtmm) REVERT: A 680 ASN cc_start: 0.8456 (t0) cc_final: 0.8221 (t0) outliers start: 20 outliers final: 11 residues processed: 105 average time/residue: 0.3681 time to fit residues: 41.4668 Evaluate side-chains 108 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 57 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.091028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.077862 restraints weight = 15658.008| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.89 r_work: 0.3052 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 7617 Z= 0.162 Angle : 0.598 10.037 10657 Z= 0.329 Chirality : 0.041 0.239 1214 Planarity : 0.003 0.029 1042 Dihedral : 19.140 172.701 1725 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.90 % Allowed : 18.68 % Favored : 78.42 % 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: 0.87 (0.33), residues: 667 helix: 1.56 (0.29), residues: 341 sheet: -0.20 (0.59), residues: 69 loop : -0.46 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 699 TYR 0.024 0.002 TYR A 172 PHE 0.013 0.001 PHE A 400 TRP 0.019 0.003 TRP A 185 HIS 0.003 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 7617) covalent geometry : angle 0.59812 / 0.33 (10657) hydrogen bonds : bond 0.04479 / 2.94 ( 376) hydrogen bonds : angle 4.41410 / 2.93 ( 1000) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8566 (tp30) cc_final: 0.8096 (tp30) REVERT: A 175 GLU cc_start: 0.8646 (pp20) cc_final: 0.7970 (tm-30) REVERT: A 206 MET cc_start: 0.8129 (mmm) cc_final: 0.7705 (mmt) REVERT: A 230 ASP cc_start: 0.8485 (t0) cc_final: 0.8059 (t0) REVERT: A 233 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8082 (pp) REVERT: A 288 ASP cc_start: 0.8613 (t70) cc_final: 0.8335 (t70) REVERT: A 337 VAL cc_start: 0.8569 (t) cc_final: 0.8341 (p) REVERT: A 363 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7940 (mm-30) REVERT: A 488 ASP cc_start: 0.8483 (p0) cc_final: 0.7946 (p0) REVERT: A 502 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8822 (mtmm) REVERT: A 680 ASN cc_start: 0.8361 (t0) cc_final: 0.8135 (t0) outliers start: 18 outliers final: 10 residues processed: 105 average time/residue: 0.3465 time to fit residues: 38.8673 Evaluate side-chains 106 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.091498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.078334 restraints weight = 15803.546| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.91 r_work: 0.3061 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 7617 Z= 0.156 Angle : 0.614 12.694 10657 Z= 0.334 Chirality : 0.041 0.233 1214 Planarity : 0.003 0.028 1042 Dihedral : 19.114 173.166 1725 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.42 % Allowed : 19.65 % Favored : 77.94 % 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: 0.85 (0.33), residues: 667 helix: 1.54 (0.29), residues: 341 sheet: -0.21 (0.59), residues: 69 loop : -0.47 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 440 TYR 0.026 0.001 TYR A 172 PHE 0.012 0.001 PHE A 599 TRP 0.020 0.002 TRP A 185 HIS 0.003 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 ( 7617) covalent geometry : angle 0.61376 / 0.33 (10657) hydrogen bonds : bond 0.04474 / 2.92 ( 376) hydrogen bonds : angle 4.38627 / 2.91 ( 1000) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8563 (tp30) cc_final: 0.8089 (tp30) REVERT: A 206 MET cc_start: 0.8125 (mmm) cc_final: 0.7689 (mmt) REVERT: A 230 ASP cc_start: 0.8478 (t0) cc_final: 0.8053 (t0) REVERT: A 233 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8057 (pp) REVERT: A 288 ASP cc_start: 0.8609 (t70) cc_final: 0.8329 (t70) REVERT: A 337 VAL cc_start: 0.8535 (t) cc_final: 0.8298 (p) REVERT: A 488 ASP cc_start: 0.8496 (p0) cc_final: 0.7977 (p0) REVERT: A 650 TYR cc_start: 0.8144 (m-10) cc_final: 0.7938 (m-10) REVERT: A 680 ASN cc_start: 0.8363 (t0) cc_final: 0.8141 (t0) outliers start: 15 outliers final: 9 residues processed: 105 average time/residue: 0.3593 time to fit residues: 40.4302 Evaluate side-chains 105 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 0.0970 chunk 65 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.092838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.079701 restraints weight = 15682.977| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.89 r_work: 0.3091 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7617 Z= 0.141 Angle : 0.604 11.627 10657 Z= 0.331 Chirality : 0.041 0.224 1214 Planarity : 0.003 0.026 1042 Dihedral : 19.064 174.062 1725 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.09 % Allowed : 19.81 % Favored : 78.10 % 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: 0.91 (0.33), residues: 667 helix: 1.63 (0.29), residues: 341 sheet: -0.21 (0.58), residues: 69 loop : -0.49 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 450 TYR 0.023 0.001 TYR A 172 PHE 0.010 0.001 PHE A 603 TRP 0.017 0.002 TRP A 185 HIS 0.003 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 7617) covalent geometry : angle 0.60372 / 0.33 (10657) hydrogen bonds : bond 0.04345 / 2.80 ( 376) hydrogen bonds : angle 4.33007 / 2.88 ( 1000) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1884.96 seconds wall clock time: 32 minutes 56.83 seconds (1976.83 seconds total)