Starting phenix.real_space_refine on Fri Sep 11 04:26:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dc2_27320/09_2026/8dc2_27320.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dc2_27320/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8dc2_27320/09_2026/8dc2_27320.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dc2_27320/09_2026/8dc2_27320.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dc2_27320/09_2026/8dc2_27320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dc2_27320/09_2026/8dc2_27320.map" model { file = "/net/cci-nas-00/data/ceres_data/8dc2_27320/09_2026/8dc2_27320.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dc2_27320/09_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-2.2.1-6174/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: {'RNAv2': 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: 1.66, per 1000 atoms: 0.23 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: 0.72 Conformation dependent library (CDL) restraints added in 338.4 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: 0.93 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: 1.67 Time building geometry restraints manager: 0.85 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: 9900 1.18 - 2.36: 526 2.36 - 3.54: 182 3.54 - 4.72: 36 4.72 - 5.90: 13 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 - 31.97: 4053 31.97 - 63.94: 305 63.94 - 95.91: 13 95.91 - 127.88: 0 127.88 - 159.84: 2 Dihedral angle restraints: 4373 sinusoidal: 2376 harmonic: 1997 Sorted by residual: dihedral pdb=" C4' A B -5 " pdb=" C3' A B -5 " pdb=" C2' A B -5 " pdb=" C1' A B -5 " ideal model delta sinusoidal sigma weight residual 36.35 -38.42 74.77 1 3.10e+00 1.04e-01 7.37e+02 dihedral pdb=" C4' G B -15 " pdb=" C3' G B -15 " pdb=" C2' G B -15 " pdb=" C1' G B -15 " ideal model delta sinusoidal sigma weight residual 36.34 -36.68 73.03 1 3.10e+00 1.04e-01 7.07e+02 dihedral pdb=" C4' A B -4 " pdb=" C3' A B -4 " pdb=" C2' A B -4 " pdb=" C1' A B -4 " ideal model delta sinusoidal sigma weight residual 36.34 -36.55 72.89 1 3.10e+00 1.04e-01 7.05e+02 ... (remaining 4370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1000 0.062 - 0.124: 143 0.124 - 0.186: 4 0.186 - 0.248: 52 0.248 - 0.310: 15 Chirality restraints: 1214 Sorted by residual: chirality pdb=" C2' C B -3 " pdb=" C3' C B -3 " pdb=" O2' C B -3 " pdb=" C1' C B -3 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C2' A B -5 " pdb=" C3' A B -5 " pdb=" O2' A B -5 " pdb=" C1' A B -5 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C2' A B -4 " pdb=" C3' A B -4 " pdb=" O2' A B -4 " pdb=" C1' A B -4 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.28 2.00e-01 2.50e+01 2.03e+00 ... (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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.310 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.280 ------------------------------------------------------------------------------- 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= 0.265 Angle : 0.694 5.898 10657 Z= 0.425 Chirality : 0.069 0.310 1214 Planarity : 0.003 0.029 1042 Dihedral : 18.983 159.845 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 0.00367 / 0.27 ( 7617) covalent geometry : angle 0.69437 / 0.42 (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 : 0.171 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: 0.4506 time to fit residues: 64.5989 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 : 0.275 ------------------------------------------------------------------------------- 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: 10.0000 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 = 0.3376 r_free = 0.3376 target = 0.090199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.077158 restraints weight = 15704.327| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.85 r_work: 0.3043 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 7617 Z= 0.283 Angle : 1.078 20.508 10657 Z= 0.477 Chirality : 0.099 1.132 1214 Planarity : 0.004 0.029 1042 Dihedral : 19.966 158.548 1727 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.74 % Allowed : 10.14 % Favored : 87.12 % 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: 0.96 (0.33), residues: 667 helix: 1.68 (0.29), residues: 334 sheet: 0.27 (0.58), residues: 70 loop : -0.60 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 239 TYR 0.021 0.002 TYR A 133 PHE 0.015 0.002 PHE A 613 TRP 0.033 0.004 TRP A 185 HIS 0.007 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.28 ( 7617) covalent geometry : angle 1.07845 / 0.48 (10657) hydrogen bonds : bond 0.05397 / 3.66 ( 376) hydrogen bonds : angle 4.71054 / 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 125 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8632 (tp30) cc_final: 0.8380 (tp30) REVERT: A 206 MET cc_start: 0.8079 (mmm) cc_final: 0.7512 (mmt) REVERT: A 230 ASP cc_start: 0.8497 (t0) cc_final: 0.8078 (t0) REVERT: A 233 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8093 (pp) REVERT: A 288 ASP cc_start: 0.8537 (t70) cc_final: 0.8315 (t70) REVERT: A 363 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: A 488 ASP cc_start: 0.8560 (p0) cc_final: 0.8030 (p0) REVERT: A 680 ASN cc_start: 0.8543 (t0) cc_final: 0.8324 (t0) REVERT: A 704 LYS cc_start: 0.7002 (OUTLIER) cc_final: 0.5595 (ttmt) outliers start: 17 outliers final: 6 residues processed: 114 average time/residue: 0.4707 time to fit residues: 57.3252 Evaluate side-chains 106 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 621 ILE 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: 0.1980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.090616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.077488 restraints weight = 15607.756| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.86 r_work: 0.3041 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 7617 Z= 0.225 Angle : 0.827 10.954 10657 Z= 0.389 Chirality : 0.067 0.722 1214 Planarity : 0.004 0.028 1042 Dihedral : 20.080 156.279 1725 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.90 % Allowed : 13.53 % Favored : 83.57 % 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: 338 sheet: 0.10 (0.59), residues: 71 loop : -0.59 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 402 TYR 0.022 0.002 TYR A 133 PHE 0.021 0.002 PHE A 396 TRP 0.013 0.002 TRP A 185 HIS 0.003 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.23 ( 7617) covalent geometry : angle 0.82731 / 0.39 (10657) hydrogen bonds : bond 0.04950 / 3.33 ( 376) hydrogen bonds : angle 4.58354 / 3.07 ( 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 124 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8607 (tp30) cc_final: 0.8220 (tp30) REVERT: A 206 MET cc_start: 0.8126 (mmm) cc_final: 0.7582 (mmt) REVERT: A 230 ASP cc_start: 0.8478 (t0) cc_final: 0.8027 (t0) REVERT: A 233 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8074 (pp) REVERT: A 288 ASP cc_start: 0.8590 (t70) cc_final: 0.8331 (t70) REVERT: A 337 VAL cc_start: 0.8698 (t) cc_final: 0.8437 (p) REVERT: A 363 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: A 488 ASP cc_start: 0.8494 (p0) cc_final: 0.7984 (p0) REVERT: A 680 ASN cc_start: 0.8430 (t0) cc_final: 0.8181 (t0) outliers start: 18 outliers final: 7 residues processed: 114 average time/residue: 0.4387 time to fit residues: 53.5541 Evaluate side-chains 109 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 19 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 677 ASN ** 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 = 0.3405 r_free = 0.3405 target = 0.091928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.078684 restraints weight = 15812.886| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.89 r_work: 0.3062 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7617 Z= 0.168 Angle : 0.742 11.057 10657 Z= 0.356 Chirality : 0.060 0.647 1214 Planarity : 0.003 0.028 1042 Dihedral : 20.186 163.958 1725 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.42 % Allowed : 15.30 % 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: 0.97 (0.33), residues: 667 helix: 1.70 (0.29), residues: 339 sheet: 0.05 (0.59), residues: 69 loop : -0.57 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 402 TYR 0.020 0.001 TYR A 133 PHE 0.020 0.002 PHE A 396 TRP 0.011 0.002 TRP A 185 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 ( 7617) covalent geometry : angle 0.74230 / 0.36 (10657) hydrogen bonds : bond 0.04525 / 3.02 ( 376) hydrogen bonds : angle 4.45141 / 2.98 ( 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 120 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8543 (tp30) cc_final: 0.8154 (tp30) REVERT: A 206 MET cc_start: 0.8120 (mmm) cc_final: 0.7581 (mmt) REVERT: A 230 ASP cc_start: 0.8361 (t0) cc_final: 0.7965 (t0) REVERT: A 233 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8031 (pp) REVERT: A 288 ASP cc_start: 0.8511 (t70) cc_final: 0.8254 (t70) REVERT: A 337 VAL cc_start: 0.8659 (t) cc_final: 0.8403 (p) REVERT: A 363 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7629 (mt-10) REVERT: A 488 ASP cc_start: 0.8385 (p0) cc_final: 0.7842 (p0) REVERT: A 680 ASN cc_start: 0.8452 (t0) cc_final: 0.8237 (t0) outliers start: 15 outliers final: 7 residues processed: 111 average time/residue: 0.4304 time to fit residues: 51.4364 Evaluate side-chains 105 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 50 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN A 695 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.089613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.076483 restraints weight = 15823.137| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.88 r_work: 0.3022 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 7617 Z= 0.239 Angle : 0.765 10.255 10657 Z= 0.368 Chirality : 0.060 0.619 1214 Planarity : 0.003 0.031 1042 Dihedral : 20.338 172.669 1725 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.54 % Allowed : 15.14 % 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: 0.84 (0.33), residues: 667 helix: 1.59 (0.29), residues: 341 sheet: -0.05 (0.60), residues: 69 loop : -0.63 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 440 TYR 0.022 0.002 TYR A 172 PHE 0.013 0.002 PHE A 604 TRP 0.011 0.002 TRP A 185 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.24 ( 7617) covalent geometry : angle 0.76544 / 0.37 (10657) hydrogen bonds : bond 0.04804 / 3.23 ( 376) hydrogen bonds : angle 4.50615 / 3.02 ( 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 122 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.250 Fit side-chains REVERT: A 59 GLU cc_start: 0.8626 (tp30) cc_final: 0.8180 (tp30) REVERT: A 175 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8164 (tm-30) REVERT: A 206 MET cc_start: 0.8141 (mmm) cc_final: 0.7728 (mmt) REVERT: A 230 ASP cc_start: 0.8489 (t0) cc_final: 0.8060 (t0) REVERT: A 233 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8063 (pp) REVERT: A 288 ASP cc_start: 0.8610 (t70) cc_final: 0.8338 (t70) REVERT: A 337 VAL cc_start: 0.8735 (t) cc_final: 0.8495 (p) REVERT: A 363 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8054 (mm-30) REVERT: A 399 LEU cc_start: 0.8867 (mp) cc_final: 0.8644 (mm) REVERT: A 488 ASP cc_start: 0.8488 (p0) cc_final: 0.7943 (p0) REVERT: A 680 ASN cc_start: 0.8495 (t0) cc_final: 0.8215 (t0) REVERT: A 704 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.5532 (ttmt) outliers start: 22 outliers final: 9 residues processed: 110 average time/residue: 0.4591 time to fit residues: 54.1920 Evaluate side-chains 110 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 167 MET 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 704 LYS 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: 4.9990 chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.091111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.078036 restraints weight = 15648.155| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.88 r_work: 0.3050 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 7617 Z= 0.171 Angle : 0.733 9.448 10657 Z= 0.353 Chirality : 0.058 0.600 1214 Planarity : 0.003 0.030 1042 Dihedral : 20.287 177.033 1725 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.90 % Allowed : 17.23 % Favored : 79.87 % 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: 1.51 (0.28), residues: 347 sheet: -0.10 (0.59), residues: 69 loop : -0.51 (0.40), residues: 251 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 0.014 0.001 PHE A 396 TRP 0.055 0.004 TRP A 185 HIS 0.003 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 ( 7617) covalent geometry : angle 0.73321 / 0.35 (10657) hydrogen bonds : bond 0.04496 / 3.00 ( 376) hydrogen bonds : angle 4.43256 / 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 122 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8576 (tp30) cc_final: 0.8119 (tp30) REVERT: A 206 MET cc_start: 0.8132 (mmm) cc_final: 0.7724 (mmt) REVERT: A 230 ASP cc_start: 0.8488 (t0) cc_final: 0.8056 (t0) REVERT: A 233 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8056 (pp) REVERT: A 288 ASP cc_start: 0.8586 (t70) cc_final: 0.8316 (t70) REVERT: A 337 VAL cc_start: 0.8537 (t) cc_final: 0.8289 (p) REVERT: A 363 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7978 (mm-30) REVERT: A 399 LEU cc_start: 0.8766 (mp) cc_final: 0.8552 (mm) REVERT: A 488 ASP cc_start: 0.8465 (p0) cc_final: 0.7918 (p0) REVERT: A 680 ASN cc_start: 0.8451 (t0) cc_final: 0.8183 (t0) outliers start: 18 outliers final: 8 residues processed: 112 average time/residue: 0.4529 time to fit residues: 54.4038 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 : 0.237 ------------------------------------------------------------------------------- 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 253 SER 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 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: 3.9990 chunk 3 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 23 optimal weight: 0.0980 chunk 61 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 ASN A 347 ASN ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.090282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.077237 restraints weight = 15773.123| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.87 r_work: 0.3033 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 7617 Z= 0.224 Angle : 0.768 9.447 10657 Z= 0.369 Chirality : 0.058 0.600 1214 Planarity : 0.003 0.030 1042 Dihedral : 20.300 178.089 1725 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.90 % Allowed : 17.55 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.81 (0.33), residues: 667 helix: 1.57 (0.28), residues: 341 sheet: -0.15 (0.60), residues: 69 loop : -0.63 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.021 0.002 TYR A 133 PHE 0.014 0.002 PHE A 396 TRP 0.040 0.004 TRP A 185 HIS 0.003 0.001 HIS A 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.22 ( 7617) covalent geometry : angle 0.76772 / 0.37 (10657) hydrogen bonds : bond 0.04720 / 3.15 ( 376) hydrogen bonds : angle 4.49653 / 3.01 ( 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 116 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8583 (tp30) cc_final: 0.8113 (tp30) REVERT: A 175 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8010 (tm-30) REVERT: A 206 MET cc_start: 0.8141 (mmm) cc_final: 0.7707 (mmt) REVERT: A 230 ASP cc_start: 0.8484 (t0) cc_final: 0.8061 (t0) REVERT: A 233 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8079 (pp) REVERT: A 288 ASP cc_start: 0.8620 (t70) cc_final: 0.8326 (t70) REVERT: A 337 VAL cc_start: 0.8586 (t) cc_final: 0.8330 (p) REVERT: A 363 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7943 (mm-30) REVERT: A 399 LEU cc_start: 0.8789 (mp) cc_final: 0.8563 (mm) REVERT: A 488 ASP cc_start: 0.8478 (p0) cc_final: 0.7941 (p0) REVERT: A 680 ASN cc_start: 0.8485 (t0) cc_final: 0.8218 (t0) outliers start: 18 outliers final: 9 residues processed: 108 average time/residue: 0.4399 time to fit residues: 51.1202 Evaluate side-chains 107 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 165 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 346 THR 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: 0.1980 chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3388 r_free = 0.3388 target = 0.091109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.077919 restraints weight = 15923.032| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.91 r_work: 0.3049 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 7617 Z= 0.180 Angle : 0.745 9.239 10657 Z= 0.359 Chirality : 0.057 0.587 1214 Planarity : 0.003 0.029 1042 Dihedral : 20.207 179.657 1725 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.42 % Allowed : 18.84 % Favored : 78.74 % 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: 0.83 (0.33), residues: 667 helix: 1.49 (0.28), residues: 347 sheet: -0.15 (0.60), residues: 69 loop : -0.50 (0.41), residues: 251 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 0.017 0.001 PHE A 396 TRP 0.029 0.003 TRP A 185 HIS 0.002 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 ( 7617) covalent geometry : angle 0.74541 / 0.36 (10657) hydrogen bonds : bond 0.04527 / 3.00 ( 376) hydrogen bonds : angle 4.43885 / 2.97 ( 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 112 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8571 (tp30) cc_final: 0.8098 (tp30) REVERT: A 175 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8136 (tm-30) REVERT: A 206 MET cc_start: 0.8153 (mmm) cc_final: 0.7749 (mmt) REVERT: A 230 ASP cc_start: 0.8479 (t0) cc_final: 0.8061 (t0) REVERT: A 233 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8064 (pp) REVERT: A 288 ASP cc_start: 0.8619 (t70) cc_final: 0.8343 (t70) REVERT: A 337 VAL cc_start: 0.8484 (t) cc_final: 0.8226 (p) REVERT: A 363 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7956 (mm-30) REVERT: A 399 LEU cc_start: 0.8725 (mp) cc_final: 0.8515 (mm) REVERT: A 488 ASP cc_start: 0.8463 (p0) cc_final: 0.7915 (p0) REVERT: A 680 ASN cc_start: 0.8471 (t0) cc_final: 0.8214 (t0) outliers start: 15 outliers final: 9 residues processed: 105 average time/residue: 0.4482 time to fit residues: 50.4946 Evaluate side-chains 106 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 57 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3400 r_free = 0.3400 target = 0.091823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.078622 restraints weight = 15648.066| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.88 r_work: 0.3062 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7617 Z= 0.163 Angle : 0.738 9.057 10657 Z= 0.357 Chirality : 0.056 0.586 1214 Planarity : 0.003 0.028 1042 Dihedral : 20.156 178.688 1725 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.42 % Allowed : 19.48 % 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: 0.83 (0.33), residues: 667 helix: 1.47 (0.28), residues: 347 sheet: -0.14 (0.59), residues: 69 loop : -0.48 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 402 TYR 0.026 0.002 TYR A 172 PHE 0.020 0.001 PHE A 396 TRP 0.026 0.003 TRP A 185 HIS 0.003 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 7617) covalent geometry : angle 0.73827 / 0.36 (10657) hydrogen bonds : bond 0.04482 / 2.96 ( 376) hydrogen bonds : angle 4.42121 / 2.94 ( 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 112 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8547 (tp30) cc_final: 0.8082 (tp30) REVERT: A 175 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8119 (tm-30) REVERT: A 206 MET cc_start: 0.8157 (mmm) cc_final: 0.7743 (mmt) REVERT: A 230 ASP cc_start: 0.8468 (t0) cc_final: 0.8041 (t0) REVERT: A 233 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8057 (pp) REVERT: A 288 ASP cc_start: 0.8611 (t70) cc_final: 0.8329 (t70) REVERT: A 399 LEU cc_start: 0.8704 (mp) cc_final: 0.8501 (mm) REVERT: A 488 ASP cc_start: 0.8452 (p0) cc_final: 0.7919 (p0) REVERT: A 680 ASN cc_start: 0.8437 (t0) cc_final: 0.8175 (t0) outliers start: 15 outliers final: 10 residues processed: 105 average time/residue: 0.4300 time to fit residues: 48.5174 Evaluate side-chains 107 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 26 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3412 r_free = 0.3412 target = 0.092269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.079211 restraints weight = 15771.955| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.89 r_work: 0.3074 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7617 Z= 0.156 Angle : 0.730 8.618 10657 Z= 0.354 Chirality : 0.056 0.590 1214 Planarity : 0.003 0.028 1042 Dihedral : 20.117 178.359 1725 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.61 % Allowed : 20.29 % 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: 0.87 (0.33), residues: 667 helix: 1.50 (0.28), residues: 347 sheet: -0.11 (0.59), residues: 69 loop : -0.45 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 440 TYR 0.024 0.001 TYR A 172 PHE 0.020 0.001 PHE A 396 TRP 0.024 0.003 TRP A 185 HIS 0.002 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 ( 7617) covalent geometry : angle 0.72994 / 0.35 (10657) hydrogen bonds : bond 0.04444 / 2.92 ( 376) hydrogen bonds : angle 4.40048 / 2.93 ( 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 105 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8516 (tp30) cc_final: 0.8047 (tp30) REVERT: A 175 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8040 (tm-30) REVERT: A 206 MET cc_start: 0.8163 (mmm) cc_final: 0.7744 (mmt) REVERT: A 230 ASP cc_start: 0.8416 (t0) cc_final: 0.7998 (t0) REVERT: A 233 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8036 (pp) REVERT: A 288 ASP cc_start: 0.8585 (t70) cc_final: 0.8298 (t70) REVERT: A 488 ASP cc_start: 0.8495 (p0) cc_final: 0.7987 (p0) REVERT: A 650 TYR cc_start: 0.7948 (m-10) cc_final: 0.7681 (m-10) REVERT: A 680 ASN cc_start: 0.8278 (t0) cc_final: 0.8062 (t0) outliers start: 10 outliers final: 8 residues processed: 101 average time/residue: 0.4565 time to fit residues: 49.4776 Evaluate side-chains 101 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET 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: 5.9990 chunk 13 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 347 ASN ** 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 = 0.3403 r_free = 0.3403 target = 0.091696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.078628 restraints weight = 15666.235| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.88 r_work: 0.3066 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2121 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= 0.180 Angle : 0.746 8.382 10657 Z= 0.361 Chirality : 0.056 0.595 1214 Planarity : 0.003 0.027 1042 Dihedral : 20.141 178.740 1725 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.77 % Allowed : 20.29 % 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: 0.80 (0.33), residues: 667 helix: 1.45 (0.28), residues: 347 sheet: -0.13 (0.60), residues: 67 loop : -0.52 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 450 TYR 0.024 0.002 TYR A 172 PHE 0.022 0.001 PHE A 396 TRP 0.026 0.003 TRP A 185 HIS 0.003 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 ( 7617) covalent geometry : angle 0.74559 / 0.36 (10657) hydrogen bonds : bond 0.04530 / 2.98 ( 376) hydrogen bonds : angle 4.42240 / 2.96 ( 1000) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2218.46 seconds wall clock time: 38 minutes 48.95 seconds (2328.95 seconds total)