Starting phenix.real_space_refine on Tue Aug 4 20:40:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v7z_64826/08_2026/9v7z_64826.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v7z_64826/08_2026/9v7z_64826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v7z_64826/08_2026/9v7z_64826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v7z_64826/08_2026/9v7z_64826.map" model { file = "/net/cci-nas-00/data/ceres_data/9v7z_64826/08_2026/9v7z_64826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v7z_64826/08_2026/9v7z_64826.cif" } resolution = 2.97 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= -0.000 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 23 5.49 5 Mg 3 5.21 5 S 15 5.16 5 C 4034 2.51 5 N 1191 2.21 5 O 1275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6541 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 6044 Classifications: {'peptide': 757} Link IDs: {'PTRANS': 42, 'TRANS': 714} Chain: "B" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 296 Classifications: {'DNA': 14} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 13} Chain: "C" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 7} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.51, per 1000 atoms: 0.23 Number of scatterers: 6541 At special positions: 0 Unit cell: (79.143, 94.461, 101.269, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 15 16.00 P 23 15.00 Mg 3 11.99 O 1275 8.00 N 1191 7.00 C 4034 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: 0.55 Conformation dependent library (CDL) restraints added in 344.8 milliseconds 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 8 sheets defined 30.1% alpha, 23.4% beta 2 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 37 through 54 Processing helix chain 'A' and resid 109 through 130 removed outlier: 3.582A pdb=" N ALA A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 253 through 261 Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 312 through 325 removed outlier: 3.719A pdb=" N GLU A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 392 removed outlier: 3.642A pdb=" N LYS A 384 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N MET A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 431 Processing helix chain 'A' and resid 451 through 464 removed outlier: 3.599A pdb=" N LEU A 455 " --> pdb=" O GLY A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 491 Processing helix chain 'A' and resid 501 through 509 Processing helix chain 'A' and resid 516 through 530 Processing helix chain 'A' and resid 587 through 606 Processing helix chain 'A' and resid 621 through 638 removed outlier: 3.508A pdb=" N ALA A 627 " --> pdb=" O ASN A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 734 Processing helix chain 'A' and resid 749 through 753 Processing sheet with id=AA1, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.647A pdb=" N PHE A 344 " --> pdb=" O ALA A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 139 removed outlier: 6.828A pdb=" N LEU A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ARG A 162 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL A 330 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 3.594A pdb=" N VAL A 58 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA A 67 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU A 23 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLU A 99 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL A 25 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 219 through 222 removed outlier: 3.604A pdb=" N CYS A 230 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N PHE A 232 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ARG A 276 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A 234 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ALA A 272 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 275 " --> pdb=" O TRP A 284 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP A 284 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 245 through 247 Processing sheet with id=AA6, first strand: chain 'A' and resid 363 through 365 removed outlier: 3.581A pdb=" N GLN A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 436 through 442 removed outlier: 6.853A pdb=" N LEU A 402 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE A 440 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU A 404 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TYR A 442 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR A 406 " --> pdb=" O TYR A 442 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP A 401 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL A 472 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL A 403 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL A 474 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 405 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 568 through 575 removed outlier: 6.225A pdb=" N PHE A 545 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N HIS A 615 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N MET A 547 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 649 " --> pdb=" O THR A 714 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER A 679 " --> pdb=" O THR A 691 " (cutoff:3.500A) 257 hydrogen bonds defined for protein. 726 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 8 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1818 1.33 - 1.45: 1197 1.45 - 1.57: 3629 1.57 - 1.69: 44 1.69 - 1.81: 23 Bond restraints: 6711 Sorted by residual: bond pdb=" C3' DT B 9 " pdb=" C2' DT B 9 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.41e+00 bond pdb=" C3' DG B 11 " pdb=" C2' DG B 11 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.02e+00 bond pdb=" C1' DT B 14 " pdb=" N1 DT B 14 " ideal model delta sigma weight residual 1.468 1.496 -0.028 1.40e-02 5.10e+03 4.09e+00 bond pdb=" C1' DT B 13 " pdb=" N1 DT B 13 " ideal model delta sigma weight residual 1.468 1.496 -0.028 1.40e-02 5.10e+03 3.89e+00 bond pdb=" O4' DT B 9 " pdb=" C1' DT B 9 " ideal model delta sigma weight residual 1.420 1.399 0.021 1.10e-02 8.26e+03 3.81e+00 ... (remaining 6706 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 8905 1.47 - 2.94: 270 2.94 - 4.41: 29 4.41 - 5.88: 2 5.88 - 7.35: 2 Bond angle restraints: 9208 Sorted by residual: angle pdb=" N3 DT B 1 " pdb=" C4 DT B 1 " pdb=" O4 DT B 1 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT B 9 " pdb=" C4 DT B 9 " pdb=" O4 DT B 9 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT B 6 " pdb=" C4 DT B 6 " pdb=" O4 DT B 6 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT B 14 " pdb=" C4 DT B 14 " pdb=" O4 DT B 14 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT B 13 " pdb=" C4 DT B 13 " pdb=" O4 DT B 13 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.61e+01 ... (remaining 9203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.07: 3925 35.07 - 70.15: 82 70.15 - 105.22: 9 105.22 - 140.30: 0 140.30 - 175.37: 1 Dihedral angle restraints: 4017 sinusoidal: 1834 harmonic: 2183 Sorted by residual: dihedral pdb=" C4' DG B 11 " pdb=" C3' DG B 11 " pdb=" O3' DG B 11 " pdb=" P DG B 12 " ideal model delta sinusoidal sigma weight residual -140.00 35.37 -175.37 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA HIS A 206 " pdb=" C HIS A 206 " pdb=" N VAL A 207 " pdb=" CA VAL A 207 " ideal model delta harmonic sigma weight residual -180.00 -162.05 -17.95 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" O4' U C 7 " pdb=" C1' U C 7 " pdb=" N1 U C 7 " pdb=" C2 U C 7 " ideal model delta sinusoidal sigma weight residual -160.00 -118.40 -41.60 1 1.50e+01 4.44e-03 1.08e+01 ... (remaining 4014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 689 0.033 - 0.065: 202 0.065 - 0.098: 74 0.098 - 0.131: 47 0.131 - 0.163: 9 Chirality restraints: 1021 Sorted by residual: chirality pdb=" CB VAL A 207 " pdb=" CA VAL A 207 " pdb=" CG1 VAL A 207 " pdb=" CG2 VAL A 207 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA GLU A 52 " pdb=" N GLU A 52 " pdb=" C GLU A 52 " pdb=" CB GLU A 52 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" C2' C C 12 " pdb=" C3' C C 12 " pdb=" O2' C C 12 " pdb=" C1' C C 12 " both_signs ideal model delta sigma weight residual False -2.62 -2.75 0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 1018 not shown) Planarity restraints: 1128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 87 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO A 88 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 399 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO A 400 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 400 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 400 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 533 " 0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 534 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 534 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 534 " 0.022 5.00e-02 4.00e+02 ... (remaining 1125 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 58 2.64 - 3.20: 5363 3.20 - 3.77: 9568 3.77 - 4.33: 13881 4.33 - 4.90: 22692 Nonbonded interactions: 51562 Sorted by model distance: nonbonded pdb=" OP2 U C 7 " pdb="MG MG A 801 " model vdw 2.070 2.170 nonbonded pdb=" OD1 ASP A 35 " pdb=" OG1 THR A 38 " model vdw 2.261 3.040 nonbonded pdb=" OE2 GLU A 375 " pdb=" NH2 ARG A 379 " model vdw 2.303 3.120 nonbonded pdb=" OH TYR A 185 " pdb=" O VAL A 307 " model vdw 2.313 3.040 nonbonded pdb=" OP2 DT B 1 " pdb="MG MG B 101 " model vdw 2.328 2.170 ... (remaining 51557 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.160 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:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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 : 0.003 0.048 6711 Z= 0.209 Angle : 0.583 7.350 9208 Z= 0.375 Chirality : 0.043 0.163 1021 Planarity : 0.005 0.060 1128 Dihedral : 14.732 175.374 2611 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.30), residues: 755 helix: 1.66 (0.36), residues: 216 sheet: 0.52 (0.39), residues: 176 loop : -0.45 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 276 TYR 0.017 0.002 TYR A 258 PHE 0.011 0.001 PHE A 323 TRP 0.019 0.002 TRP A 140 HIS 0.007 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.21 ( 6711) covalent geometry : angle 0.58343 / 0.38 ( 9208) hydrogen bonds : bond 0.19901 / 13.98 ( 261) hydrogen bonds : angle 6.93493 / 4.92 ( 734) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.171 Fit side-chains REVERT: A 54 LYS cc_start: 0.6867 (mmmt) cc_final: 0.6634 (mmmm) REVERT: A 520 ARG cc_start: 0.7344 (ttp-170) cc_final: 0.6984 (ttm-80) outliers start: 0 outliers final: 2 residues processed: 88 average time/residue: 0.5638 time to fit residues: 52.0774 Evaluate side-chains 67 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 ASN A 482 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.181208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.132754 restraints weight = 7061.811| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.31 r_work: 0.3143 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 6711 Z= 0.180 Angle : 0.568 5.643 9208 Z= 0.310 Chirality : 0.043 0.155 1021 Planarity : 0.005 0.060 1128 Dihedral : 14.230 170.082 1135 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.16 % Allowed : 6.80 % Favored : 91.04 % 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: 0.61 (0.30), residues: 755 helix: 1.89 (0.35), residues: 218 sheet: 0.51 (0.39), residues: 173 loop : -0.54 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 435 TYR 0.019 0.002 TYR A 377 PHE 0.014 0.002 PHE A 545 TRP 0.016 0.002 TRP A 136 HIS 0.009 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 ( 6711) covalent geometry : angle 0.56773 / 0.31 ( 9208) hydrogen bonds : bond 0.04927 / 3.46 ( 261) hydrogen bonds : angle 5.27876 / 3.74 ( 734) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 147 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: A 436 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8266 (mm) REVERT: A 520 ARG cc_start: 0.7745 (ttp-170) cc_final: 0.7167 (ttm-80) outliers start: 14 outliers final: 5 residues processed: 76 average time/residue: 0.4676 time to fit residues: 37.4444 Evaluate side-chains 72 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 436 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 20 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.178476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.125888 restraints weight = 6967.484| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.25 r_work: 0.3063 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 6711 Z= 0.159 Angle : 0.540 5.996 9208 Z= 0.293 Chirality : 0.043 0.152 1021 Planarity : 0.005 0.057 1128 Dihedral : 14.228 170.494 1131 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.70 % Allowed : 10.97 % Favored : 87.33 % 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: 0.62 (0.30), residues: 755 helix: 1.97 (0.35), residues: 220 sheet: 0.37 (0.39), residues: 173 loop : -0.52 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 435 TYR 0.017 0.001 TYR A 377 PHE 0.012 0.001 PHE A 545 TRP 0.015 0.002 TRP A 136 HIS 0.009 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 6711) covalent geometry : angle 0.53958 / 0.29 ( 9208) hydrogen bonds : bond 0.04432 / 3.07 ( 261) hydrogen bonds : angle 4.98049 / 3.52 ( 734) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 147 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8277 (tm-30) REVERT: A 156 ASP cc_start: 0.8179 (m-30) cc_final: 0.7898 (m-30) REVERT: A 436 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8256 (mm) REVERT: A 490 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.7044 (ttp80) outliers start: 11 outliers final: 6 residues processed: 72 average time/residue: 0.4370 time to fit residues: 33.2518 Evaluate side-chains 69 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 1 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.178282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.126880 restraints weight = 7067.058| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.37 r_work: 0.3032 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6711 Z= 0.181 Angle : 0.555 6.811 9208 Z= 0.298 Chirality : 0.043 0.153 1021 Planarity : 0.005 0.058 1128 Dihedral : 14.259 170.763 1131 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.47 % Allowed : 10.82 % Favored : 86.71 % 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: 0.61 (0.30), residues: 755 helix: 1.92 (0.35), residues: 220 sheet: 0.30 (0.39), residues: 173 loop : -0.46 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 435 TYR 0.018 0.002 TYR A 377 PHE 0.013 0.001 PHE A 545 TRP 0.015 0.002 TRP A 136 HIS 0.009 0.002 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 ( 6711) covalent geometry : angle 0.55542 / 0.30 ( 9208) hydrogen bonds : bond 0.04362 / 3.02 ( 261) hydrogen bonds : angle 4.87508 / 3.44 ( 734) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.6668 (mmtp) cc_final: 0.6144 (mmmm) REVERT: A 147 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8094 (tm-30) REVERT: A 156 ASP cc_start: 0.8212 (m-30) cc_final: 0.7957 (m-30) REVERT: A 436 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8350 (mm) REVERT: A 490 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7134 (ttp80) outliers start: 16 outliers final: 7 residues processed: 68 average time/residue: 0.4496 time to fit residues: 32.4083 Evaluate side-chains 70 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 676 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 67 optimal weight: 0.0370 chunk 39 optimal weight: 0.0970 chunk 8 optimal weight: 0.4980 chunk 60 optimal weight: 0.0970 overall best weight: 0.2854 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.184518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.135482 restraints weight = 7094.483| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.34 r_work: 0.3106 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6711 Z= 0.103 Angle : 0.462 6.094 9208 Z= 0.257 Chirality : 0.040 0.137 1021 Planarity : 0.005 0.057 1128 Dihedral : 14.148 172.724 1131 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.39 % Allowed : 12.06 % Favored : 86.55 % 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: 0.84 (0.30), residues: 755 helix: 2.12 (0.35), residues: 220 sheet: 0.42 (0.39), residues: 173 loop : -0.31 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 435 TYR 0.015 0.001 TYR A 92 PHE 0.006 0.001 PHE A 545 TRP 0.012 0.001 TRP A 140 HIS 0.006 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 6711) covalent geometry : angle 0.46167 / 0.26 ( 9208) hydrogen bonds : bond 0.03270 / 2.26 ( 261) hydrogen bonds : angle 4.62344 / 3.26 ( 734) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 141 ASN cc_start: 0.8265 (p0) cc_final: 0.7862 (p0) REVERT: A 147 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8060 (tm-30) REVERT: A 156 ASP cc_start: 0.8131 (m-30) cc_final: 0.7922 (m-30) REVERT: A 193 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7800 (mm-30) REVERT: A 373 ILE cc_start: 0.7548 (mm) cc_final: 0.7198 (mm) REVERT: A 490 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6987 (ttp80) outliers start: 9 outliers final: 1 residues processed: 69 average time/residue: 0.4805 time to fit residues: 35.1270 Evaluate side-chains 63 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 490 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 45 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 69 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.177304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.125196 restraints weight = 7120.554| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.43 r_work: 0.3044 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 6711 Z= 0.254 Angle : 0.614 6.355 9208 Z= 0.323 Chirality : 0.046 0.158 1021 Planarity : 0.005 0.055 1128 Dihedral : 14.282 171.236 1131 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.32 % Allowed : 12.06 % Favored : 85.63 % 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: 0.57 (0.30), residues: 755 helix: 1.91 (0.36), residues: 220 sheet: 0.34 (0.40), residues: 173 loop : -0.54 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 435 TYR 0.018 0.002 TYR A 377 PHE 0.016 0.002 PHE A 545 TRP 0.015 0.002 TRP A 136 HIS 0.011 0.002 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.25 ( 6711) covalent geometry : angle 0.61412 / 0.32 ( 9208) hydrogen bonds : bond 0.04718 / 3.27 ( 261) hydrogen bonds : angle 4.82825 / 3.40 ( 734) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.6622 (mmtp) cc_final: 0.6092 (mmmm) REVERT: A 147 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: A 436 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8433 (mm) REVERT: A 490 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7137 (ttp80) outliers start: 15 outliers final: 7 residues processed: 67 average time/residue: 0.5401 time to fit residues: 38.1563 Evaluate side-chains 68 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 676 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.178449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.129280 restraints weight = 7030.132| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.53 r_work: 0.3113 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6711 Z= 0.164 Angle : 0.533 6.842 9208 Z= 0.286 Chirality : 0.042 0.154 1021 Planarity : 0.005 0.054 1128 Dihedral : 14.252 171.596 1131 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.01 % Allowed : 12.83 % Favored : 85.16 % 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: 0.58 (0.30), residues: 755 helix: 1.95 (0.36), residues: 220 sheet: 0.31 (0.39), residues: 173 loop : -0.54 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 435 TYR 0.016 0.002 TYR A 377 PHE 0.011 0.001 PHE A 545 TRP 0.016 0.002 TRP A 136 HIS 0.009 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.16 ( 6711) covalent geometry : angle 0.53277 / 0.29 ( 9208) hydrogen bonds : bond 0.04040 / 2.79 ( 261) hydrogen bonds : angle 4.75877 / 3.36 ( 734) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 147 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8087 (tm-30) REVERT: A 436 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8383 (mm) REVERT: A 490 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7098 (ttp80) outliers start: 13 outliers final: 5 residues processed: 65 average time/residue: 0.5084 time to fit residues: 34.8154 Evaluate side-chains 64 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 676 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 20 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 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 = 0.3952 r_free = 0.3952 target = 0.179599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.128315 restraints weight = 7040.135| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.52 r_work: 0.3053 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6711 Z= 0.134 Angle : 0.497 6.737 9208 Z= 0.270 Chirality : 0.041 0.147 1021 Planarity : 0.005 0.054 1128 Dihedral : 14.185 172.441 1131 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.32 % Allowed : 13.14 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.30), residues: 755 helix: 2.03 (0.36), residues: 220 sheet: 0.38 (0.39), residues: 173 loop : -0.47 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 509 TYR 0.014 0.001 TYR A 377 PHE 0.010 0.001 PHE A 545 TRP 0.014 0.001 TRP A 140 HIS 0.007 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 6711) covalent geometry : angle 0.49740 / 0.27 ( 9208) hydrogen bonds : bond 0.03641 / 2.50 ( 261) hydrogen bonds : angle 4.62771 / 3.26 ( 734) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 147 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8141 (tm-30) REVERT: A 373 ILE cc_start: 0.7826 (mm) cc_final: 0.7438 (mm) REVERT: A 436 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8387 (mm) REVERT: A 490 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7108 (ttp80) outliers start: 15 outliers final: 7 residues processed: 66 average time/residue: 0.4806 time to fit residues: 33.4870 Evaluate side-chains 66 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 47 optimal weight: 0.0270 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.179255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.129478 restraints weight = 7097.321| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.42 r_work: 0.3045 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6711 Z= 0.132 Angle : 0.495 6.102 9208 Z= 0.269 Chirality : 0.041 0.146 1021 Planarity : 0.004 0.054 1128 Dihedral : 14.152 172.530 1131 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.70 % Allowed : 14.06 % Favored : 84.23 % 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: 0.68 (0.30), residues: 755 helix: 2.03 (0.36), residues: 220 sheet: 0.38 (0.39), residues: 173 loop : -0.48 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 509 TYR 0.015 0.001 TYR A 377 PHE 0.010 0.001 PHE A 545 TRP 0.013 0.001 TRP A 140 HIS 0.008 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 6711) covalent geometry : angle 0.49496 / 0.27 ( 9208) hydrogen bonds : bond 0.03625 / 2.50 ( 261) hydrogen bonds : angle 4.58824 / 3.24 ( 734) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 147 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8120 (tm-30) REVERT: A 150 ASN cc_start: 0.7331 (t0) cc_final: 0.7103 (t0) REVERT: A 436 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8377 (mm) REVERT: A 490 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7109 (ttp80) outliers start: 11 outliers final: 6 residues processed: 65 average time/residue: 0.4675 time to fit residues: 32.0124 Evaluate side-chains 65 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.177295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.126214 restraints weight = 6950.159| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.61 r_work: 0.3093 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 6711 Z= 0.214 Angle : 0.588 6.979 9208 Z= 0.309 Chirality : 0.045 0.158 1021 Planarity : 0.005 0.057 1128 Dihedral : 14.246 171.698 1131 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.85 % Allowed : 13.91 % Favored : 84.23 % 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: 0.52 (0.30), residues: 755 helix: 1.92 (0.36), residues: 220 sheet: 0.31 (0.39), residues: 173 loop : -0.59 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 44 TYR 0.017 0.002 TYR A 377 PHE 0.014 0.002 PHE A 545 TRP 0.013 0.002 TRP A 136 HIS 0.010 0.002 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.21 ( 6711) covalent geometry : angle 0.58777 / 0.31 ( 9208) hydrogen bonds : bond 0.04381 / 3.03 ( 261) hydrogen bonds : angle 4.72075 / 3.34 ( 734) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 147 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: A 436 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8408 (mm) REVERT: A 490 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.7150 (ttp80) outliers start: 12 outliers final: 6 residues processed: 66 average time/residue: 0.4805 time to fit residues: 33.3770 Evaluate side-chains 66 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 676 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 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 = 0.3968 r_free = 0.3968 target = 0.181208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.131620 restraints weight = 7027.575| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.43 r_work: 0.3147 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 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 : 0.003 0.055 6711 Z= 0.124 Angle : 0.502 8.135 9208 Z= 0.270 Chirality : 0.041 0.155 1021 Planarity : 0.005 0.057 1128 Dihedral : 14.190 172.414 1131 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.24 % Allowed : 14.53 % Favored : 84.23 % 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: 0.66 (0.30), residues: 755 helix: 2.04 (0.36), residues: 220 sheet: 0.38 (0.39), residues: 173 loop : -0.50 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 44 TYR 0.014 0.001 TYR A 377 PHE 0.009 0.001 PHE A 662 TRP 0.014 0.001 TRP A 136 HIS 0.007 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 6711) covalent geometry : angle 0.50213 / 0.27 ( 9208) hydrogen bonds : bond 0.03567 / 2.46 ( 261) hydrogen bonds : angle 4.60224 / 3.26 ( 734) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1738.61 seconds wall clock time: 30 minutes 17.96 seconds (1817.96 seconds total)