Starting phenix.real_space_refine on Wed Mar 4 11:55:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t9g_25757/03_2026/7t9g_25757.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9g_25757/03_2026/7t9g_25757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t9g_25757/03_2026/7t9g_25757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9g_25757/03_2026/7t9g_25757.map" model { file = "/net/cci-nas-00/data/ceres_data/7t9g_25757/03_2026/7t9g_25757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9g_25757/03_2026/7t9g_25757.cif" } resolution = 2.83 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= 1.000 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 S 52 5.16 5 Na 4 4.78 5 C 4456 2.51 5 N 1046 2.21 5 O 1133 1.98 5 H 6958 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13649 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6820 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 6820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6820 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Y" 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: 2.87, per 1000 atoms: 0.21 Number of scatterers: 13649 At special positions: 0 Unit cell: (88.81, 102.09, 76.36, 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 52 16.00 Na 4 11.00 O 1133 8.00 N 1046 7.00 C 4456 6.00 H 6958 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 514.1 milliseconds 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1656 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 85.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 19 through 38 Processing helix chain 'A' and resid 42 through 62 Processing helix chain 'A' and resid 65 through 79 Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 114 removed outlier: 3.601A pdb=" N PHE A 98 " --> pdb=" O ASN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 130 through 149 removed outlier: 3.517A pdb=" N VAL A 135 " --> pdb=" O MET A 131 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TRP A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 166 removed outlier: 3.587A pdb=" N ALA A 155 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Proline residue: A 160 - end of helix Processing helix chain 'A' and resid 174 through 193 removed outlier: 3.618A pdb=" N TYR A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.592A pdb=" N ALA A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 240 removed outlier: 3.634A pdb=" N PHE A 220 " --> pdb=" O ASP A 216 " (cutoff:3.500A) Proline residue: A 223 - end of helix Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 260 through 277 Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 290 through 307 Processing helix chain 'A' and resid 310 through 318 Processing helix chain 'A' and resid 319 through 339 removed outlier: 3.771A pdb=" N LEU A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 356 removed outlier: 4.696A pdb=" N ASP A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N MET A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 373 Processing helix chain 'A' and resid 377 through 396 Proline residue: A 387 - end of helix Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.703A pdb=" N SER A 404 " --> pdb=" O PRO A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 421 through 429 Processing helix chain 'A' and resid 434 through 461 Processing helix chain 'Y' and resid 19 through 38 Processing helix chain 'Y' and resid 42 through 62 Processing helix chain 'Y' and resid 65 through 79 Proline residue: Y 74 - end of helix Processing helix chain 'Y' and resid 84 through 90 Processing helix chain 'Y' and resid 91 through 93 No H-bonds generated for 'chain 'Y' and resid 91 through 93' Processing helix chain 'Y' and resid 94 through 114 removed outlier: 3.602A pdb=" N PHE Y 98 " --> pdb=" O ASN Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 114 through 127 Processing helix chain 'Y' and resid 130 through 149 removed outlier: 3.517A pdb=" N VAL Y 135 " --> pdb=" O MET Y 131 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHE Y 136 " --> pdb=" O SER Y 132 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TRP Y 148 " --> pdb=" O LEU Y 144 " (cutoff:3.500A) Processing helix chain 'Y' and resid 151 through 166 removed outlier: 3.587A pdb=" N ALA Y 155 " --> pdb=" O ASN Y 151 " (cutoff:3.500A) Proline residue: Y 160 - end of helix Processing helix chain 'Y' and resid 174 through 193 removed outlier: 3.618A pdb=" N TYR Y 178 " --> pdb=" O GLN Y 174 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL Y 185 " --> pdb=" O VAL Y 181 " (cutoff:3.500A) Processing helix chain 'Y' and resid 200 through 211 removed outlier: 3.592A pdb=" N ALA Y 204 " --> pdb=" O SER Y 200 " (cutoff:3.500A) Processing helix chain 'Y' and resid 213 through 240 removed outlier: 3.633A pdb=" N PHE Y 220 " --> pdb=" O ASP Y 216 " (cutoff:3.500A) Proline residue: Y 223 - end of helix Proline residue: Y 230 - end of helix Processing helix chain 'Y' and resid 260 through 277 Processing helix chain 'Y' and resid 277 through 284 Processing helix chain 'Y' and resid 290 through 307 Processing helix chain 'Y' and resid 310 through 318 Processing helix chain 'Y' and resid 319 through 339 removed outlier: 3.770A pdb=" N LEU Y 323 " --> pdb=" O ASP Y 319 " (cutoff:3.500A) Processing helix chain 'Y' and resid 340 through 356 removed outlier: 4.695A pdb=" N ASP Y 351 " --> pdb=" O ASN Y 347 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N MET Y 352 " --> pdb=" O ALA Y 348 " (cutoff:3.500A) Processing helix chain 'Y' and resid 357 through 373 Processing helix chain 'Y' and resid 377 through 396 Proline residue: Y 387 - end of helix Processing helix chain 'Y' and resid 400 through 413 removed outlier: 3.703A pdb=" N SER Y 404 " --> pdb=" O PRO Y 400 " (cutoff:3.500A) Processing helix chain 'Y' and resid 417 through 420 Processing helix chain 'Y' and resid 421 through 429 Processing helix chain 'Y' and resid 434 through 461 516 hydrogen bonds defined for protein. 1542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.81 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6952 1.03 - 1.23: 6 1.23 - 1.42: 2758 1.42 - 1.61: 3984 1.61 - 1.81: 98 Bond restraints: 13798 Sorted by residual: bond pdb=" CG LEU Y 250 " pdb=" CD2 LEU Y 250 " ideal model delta sigma weight residual 1.521 1.548 -0.027 3.30e-02 9.18e+02 6.55e-01 bond pdb=" CB VAL A 427 " pdb=" CG2 VAL A 427 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.17e-01 bond pdb=" CB VAL Y 427 " pdb=" CG2 VAL Y 427 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.12e-01 bond pdb=" CG LEU A 250 " pdb=" CD2 LEU A 250 " ideal model delta sigma weight residual 1.521 1.547 -0.026 3.30e-02 9.18e+02 6.10e-01 bond pdb=" CG PRO A 423 " pdb=" CD PRO A 423 " ideal model delta sigma weight residual 1.503 1.478 0.025 3.40e-02 8.65e+02 5.20e-01 ... (remaining 13793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.90: 25062 5.90 - 11.81: 4 11.81 - 17.71: 0 17.71 - 23.62: 7 23.62 - 29.52: 11 Bond angle restraints: 25084 Sorted by residual: angle pdb=" CG LEU Y 445 " pdb=" CD2 LEU Y 445 " pdb="HD23 LEU Y 445 " ideal model delta sigma weight residual 109.00 79.48 29.52 3.00e+00 1.11e-01 9.68e+01 angle pdb=" CG LEU A 445 " pdb=" CD2 LEU A 445 " pdb="HD23 LEU A 445 " ideal model delta sigma weight residual 109.00 79.48 29.52 3.00e+00 1.11e-01 9.68e+01 angle pdb=" CG LEU A 445 " pdb=" CD2 LEU A 445 " pdb="HD22 LEU A 445 " ideal model delta sigma weight residual 109.00 79.65 29.35 3.00e+00 1.11e-01 9.57e+01 angle pdb=" CG LEU Y 445 " pdb=" CD2 LEU Y 445 " pdb="HD22 LEU Y 445 " ideal model delta sigma weight residual 109.00 79.70 29.30 3.00e+00 1.11e-01 9.54e+01 angle pdb="HD21 LEU A 445 " pdb=" CD2 LEU A 445 " pdb="HD23 LEU A 445 " ideal model delta sigma weight residual 110.00 81.03 28.97 3.00e+00 1.11e-01 9.33e+01 ... (remaining 25079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 5834 16.34 - 32.68: 447 32.68 - 49.02: 107 49.02 - 65.37: 74 65.37 - 81.71: 8 Dihedral angle restraints: 6470 sinusoidal: 3394 harmonic: 3076 Sorted by residual: dihedral pdb=" CA PHE A 396 " pdb=" C PHE A 396 " pdb=" N GLY A 397 " pdb=" CA GLY A 397 " ideal model delta harmonic sigma weight residual -180.00 -159.32 -20.68 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA PHE Y 396 " pdb=" C PHE Y 396 " pdb=" N GLY Y 397 " pdb=" CA GLY Y 397 " ideal model delta harmonic sigma weight residual -180.00 -159.38 -20.62 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA GLY Y 397 " pdb=" C GLY Y 397 " pdb=" N MET Y 398 " pdb=" CA MET Y 398 " ideal model delta harmonic sigma weight residual 180.00 159.76 20.24 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 6467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 1156 0.338 - 0.677: 0 0.677 - 1.015: 0 1.015 - 1.353: 0 1.353 - 1.691: 2 Chirality restraints: 1158 Sorted by residual: chirality pdb=" CG LEU Y 250 " pdb=" CB LEU Y 250 " pdb=" CD1 LEU Y 250 " pdb=" CD2 LEU Y 250 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.15e+01 chirality pdb=" CG LEU A 250 " pdb=" CB LEU A 250 " pdb=" CD1 LEU A 250 " pdb=" CD2 LEU A 250 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.13e+01 chirality pdb=" CA VAL A 309 " pdb=" N VAL A 309 " pdb=" C VAL A 309 " pdb=" CB VAL A 309 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 1155 not shown) Planarity restraints: 1986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR Y 421 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO Y 422 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO Y 422 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO Y 422 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 421 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO A 422 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 422 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 422 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 201 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 202 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 202 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 202 " 0.018 5.00e-02 4.00e+02 ... (remaining 1983 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 672 2.19 - 2.79: 28214 2.79 - 3.40: 40397 3.40 - 4.00: 52000 4.00 - 4.60: 81891 Nonbonded interactions: 203174 Sorted by model distance: nonbonded pdb=" O MET Y 147 " pdb=" HG1 THR Y 196 " model vdw 1.590 2.450 nonbonded pdb=" O MET A 147 " pdb=" HG1 THR A 196 " model vdw 1.591 2.450 nonbonded pdb="HD22 ASN A 282 " pdb=" O PHE A 288 " model vdw 1.624 2.450 nonbonded pdb="HD22 ASN Y 282 " pdb=" O PHE Y 288 " model vdw 1.624 2.450 nonbonded pdb=" HG SER Y 146 " pdb=" O ALA Y 189 " model vdw 1.667 2.450 ... (remaining 203169 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'Y' } 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: 1.540 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: 0.070 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.120 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:9.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 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 0.033 6840 Z= 0.115 Angle : 0.550 10.025 9326 Z= 0.282 Chirality : 0.078 1.691 1158 Planarity : 0.004 0.052 1128 Dihedral : 12.680 81.706 2300 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % 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: 1.69 (0.30), residues: 886 helix: 2.01 (0.20), residues: 716 sheet: None (None), residues: 0 loop : -2.95 (0.40), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 175 TYR 0.005 0.001 TYR A 36 PHE 0.018 0.001 PHE A 100 TRP 0.013 0.001 TRP A 461 HIS 0.007 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 6840) covalent geometry : angle 0.55041 ( 9326) hydrogen bonds : bond 0.08354 ( 516) hydrogen bonds : angle 5.46481 ( 1542) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 101 average time/residue: 1.2073 time to fit residues: 128.1869 Evaluate side-chains 85 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain Y residue 157 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.102194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.090182 restraints weight = 32098.621| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.48 r_work: 0.3011 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6840 Z= 0.167 Angle : 0.577 10.699 9326 Z= 0.297 Chirality : 0.078 1.666 1158 Planarity : 0.005 0.058 1128 Dihedral : 4.890 43.954 914 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.85 % Allowed : 6.82 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.29), residues: 886 helix: 1.84 (0.20), residues: 714 sheet: None (None), residues: 0 loop : -2.89 (0.41), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Y 20 TYR 0.004 0.001 TYR Y 237 PHE 0.016 0.001 PHE Y 277 TRP 0.011 0.002 TRP A 217 HIS 0.004 0.001 HIS Y 310 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 6840) covalent geometry : angle 0.57668 ( 9326) hydrogen bonds : bond 0.04206 ( 516) hydrogen bonds : angle 4.45390 ( 1542) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.7433 (pp) REVERT: Y 20 ARG cc_start: 0.7422 (ttp-110) cc_final: 0.7205 (ttt180) REVERT: Y 240 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.7441 (pp) outliers start: 13 outliers final: 4 residues processed: 84 average time/residue: 1.2534 time to fit residues: 110.8087 Evaluate side-chains 81 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain Y residue 240 LEU Chi-restraints excluded: chain Y residue 250 LEU Chi-restraints excluded: chain Y residue 355 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.097820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.086272 restraints weight = 33281.572| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.44 r_work: 0.2957 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6840 Z= 0.169 Angle : 0.553 10.186 9326 Z= 0.283 Chirality : 0.077 1.658 1158 Planarity : 0.004 0.058 1128 Dihedral : 4.436 22.767 908 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.85 % Allowed : 7.81 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.29), residues: 886 helix: 1.87 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -3.04 (0.41), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 252 TYR 0.004 0.001 TYR Y 36 PHE 0.013 0.001 PHE Y 389 TRP 0.011 0.002 TRP Y 311 HIS 0.004 0.001 HIS Y 65 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 6840) covalent geometry : angle 0.55348 ( 9326) hydrogen bonds : bond 0.04241 ( 516) hydrogen bonds : angle 4.41122 ( 1542) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.322 Fit side-chains REVERT: A 240 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.7470 (pp) REVERT: A 313 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8259 (mt-10) REVERT: Y 20 ARG cc_start: 0.7536 (ttp-110) cc_final: 0.7272 (ttt180) REVERT: Y 42 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: Y 240 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.7467 (pp) REVERT: Y 313 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8273 (mt-10) outliers start: 13 outliers final: 5 residues processed: 86 average time/residue: 1.2209 time to fit residues: 110.4831 Evaluate side-chains 84 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 240 LEU Chi-restraints excluded: chain Y residue 250 LEU Chi-restraints excluded: chain Y residue 313 GLU Chi-restraints excluded: chain Y residue 421 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.098038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.086417 restraints weight = 32811.821| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.45 r_work: 0.2965 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6840 Z= 0.140 Angle : 0.536 10.374 9326 Z= 0.275 Chirality : 0.077 1.661 1158 Planarity : 0.004 0.059 1128 Dihedral : 4.424 23.028 908 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.42 % Allowed : 8.52 % Favored : 90.06 % 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: 1.63 (0.29), residues: 886 helix: 1.95 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -3.02 (0.41), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 20 TYR 0.004 0.001 TYR A 36 PHE 0.010 0.001 PHE A 277 TRP 0.011 0.001 TRP Y 311 HIS 0.004 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6840) covalent geometry : angle 0.53630 ( 9326) hydrogen bonds : bond 0.03988 ( 516) hydrogen bonds : angle 4.31484 ( 1542) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.365 Fit side-chains REVERT: A 240 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.7429 (pp) REVERT: Y 20 ARG cc_start: 0.7508 (ttp-110) cc_final: 0.7241 (ttt180) REVERT: Y 240 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.7437 (pp) outliers start: 10 outliers final: 7 residues processed: 80 average time/residue: 1.2904 time to fit residues: 108.6259 Evaluate side-chains 83 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain Y residue 240 LEU Chi-restraints excluded: chain Y residue 250 LEU Chi-restraints excluded: chain Y residue 355 HIS Chi-restraints excluded: chain Y residue 356 MET Chi-restraints excluded: chain Y residue 421 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 27 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 ASN Y 446 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.094559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.082876 restraints weight = 33853.035| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.47 r_work: 0.2902 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6840 Z= 0.225 Angle : 0.583 10.187 9326 Z= 0.305 Chirality : 0.078 1.649 1158 Planarity : 0.005 0.059 1128 Dihedral : 4.553 22.876 908 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.85 % Allowed : 9.80 % Favored : 88.35 % 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: 1.34 (0.29), residues: 886 helix: 1.72 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -3.01 (0.41), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 20 TYR 0.005 0.001 TYR A 237 PHE 0.016 0.002 PHE Y 277 TRP 0.013 0.002 TRP A 311 HIS 0.004 0.001 HIS Y 65 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 6840) covalent geometry : angle 0.58319 ( 9326) hydrogen bonds : bond 0.04558 ( 516) hydrogen bonds : angle 4.43844 ( 1542) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.360 Fit side-chains REVERT: A 226 MET cc_start: 0.8934 (mtm) cc_final: 0.8665 (mtp) REVERT: A 240 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.7374 (pp) REVERT: A 313 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8281 (mt-10) REVERT: Y 20 ARG cc_start: 0.7651 (ttp-110) cc_final: 0.7409 (ttt180) REVERT: Y 42 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: Y 226 MET cc_start: 0.8941 (mtm) cc_final: 0.8672 (mtp) REVERT: Y 240 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.7379 (pp) REVERT: Y 313 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8350 (mt-10) outliers start: 13 outliers final: 6 residues processed: 85 average time/residue: 1.4190 time to fit residues: 126.2785 Evaluate side-chains 85 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 240 LEU Chi-restraints excluded: chain Y residue 250 LEU Chi-restraints excluded: chain Y residue 313 GLU Chi-restraints excluded: chain Y residue 355 HIS Chi-restraints excluded: chain Y residue 421 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 66 optimal weight: 0.0060 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 20 optimal weight: 0.0870 overall best weight: 0.9978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 ASN Y 446 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.096880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.085301 restraints weight = 33333.508| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.46 r_work: 0.2949 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6840 Z= 0.123 Angle : 0.540 10.270 9326 Z= 0.274 Chirality : 0.077 1.653 1158 Planarity : 0.004 0.059 1128 Dihedral : 4.467 23.851 908 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.56 % Allowed : 11.22 % Favored : 87.22 % 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: 1.65 (0.29), residues: 886 helix: 1.98 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -3.07 (0.41), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Y 175 TYR 0.005 0.001 TYR Y 36 PHE 0.009 0.001 PHE Y 277 TRP 0.012 0.001 TRP A 311 HIS 0.004 0.001 HIS Y 65 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6840) covalent geometry : angle 0.53973 ( 9326) hydrogen bonds : bond 0.03982 ( 516) hydrogen bonds : angle 4.29238 ( 1542) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.300 Fit side-chains REVERT: A 226 MET cc_start: 0.8904 (mtm) cc_final: 0.8638 (mtp) REVERT: A 240 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7364 (pp) REVERT: Y 20 ARG cc_start: 0.7613 (ttp-110) cc_final: 0.7396 (ttt180) REVERT: Y 42 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: Y 226 MET cc_start: 0.8916 (mtm) cc_final: 0.8649 (mtp) REVERT: Y 240 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.7369 (pp) REVERT: Y 313 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8196 (mt-10) outliers start: 11 outliers final: 6 residues processed: 83 average time/residue: 1.3513 time to fit residues: 117.4559 Evaluate side-chains 84 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 240 LEU Chi-restraints excluded: chain Y residue 250 LEU Chi-restraints excluded: chain Y residue 313 GLU Chi-restraints excluded: chain Y residue 355 HIS Chi-restraints excluded: chain Y residue 421 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 39 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 67 optimal weight: 0.0270 chunk 36 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 ASN Y 446 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.095968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.084461 restraints weight = 33076.854| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.45 r_work: 0.2929 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6840 Z= 0.163 Angle : 0.549 10.226 9326 Z= 0.281 Chirality : 0.077 1.655 1158 Planarity : 0.005 0.058 1128 Dihedral : 4.467 23.357 908 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.56 % Allowed : 11.65 % Favored : 86.79 % 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: 1.64 (0.29), residues: 886 helix: 1.94 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -3.01 (0.42), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 307 TYR 0.004 0.001 TYR A 237 PHE 0.011 0.001 PHE A 277 TRP 0.013 0.002 TRP Y 311 HIS 0.003 0.001 HIS Y 65 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 6840) covalent geometry : angle 0.54895 ( 9326) hydrogen bonds : bond 0.04138 ( 516) hydrogen bonds : angle 4.29536 ( 1542) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.246 Fit side-chains REVERT: A 226 MET cc_start: 0.8910 (mtm) cc_final: 0.8642 (mtp) REVERT: A 240 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.7361 (pp) REVERT: A 313 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8275 (mt-10) REVERT: A 362 ILE cc_start: 0.8798 (pt) cc_final: 0.8555 (mt) REVERT: Y 42 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: Y 226 MET cc_start: 0.8917 (mtm) cc_final: 0.8646 (mtp) REVERT: Y 240 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7363 (pp) REVERT: Y 313 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8274 (mt-10) REVERT: Y 362 ILE cc_start: 0.8790 (pt) cc_final: 0.8540 (mt) outliers start: 11 outliers final: 6 residues processed: 83 average time/residue: 1.3694 time to fit residues: 119.0207 Evaluate side-chains 85 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 240 LEU Chi-restraints excluded: chain Y residue 250 LEU Chi-restraints excluded: chain Y residue 313 GLU Chi-restraints excluded: chain Y residue 355 HIS Chi-restraints excluded: chain Y residue 421 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 5 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.097557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.086075 restraints weight = 33234.409| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.46 r_work: 0.2953 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6840 Z= 0.117 Angle : 0.525 10.383 9326 Z= 0.265 Chirality : 0.077 1.659 1158 Planarity : 0.004 0.058 1128 Dihedral : 4.377 23.593 908 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.56 % Allowed : 11.93 % Favored : 86.51 % 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: 1.81 (0.30), residues: 886 helix: 2.09 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -3.02 (0.41), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 252 TYR 0.004 0.001 TYR Y 36 PHE 0.008 0.001 PHE A 277 TRP 0.012 0.001 TRP Y 311 HIS 0.003 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6840) covalent geometry : angle 0.52529 ( 9326) hydrogen bonds : bond 0.03851 ( 516) hydrogen bonds : angle 4.20318 ( 1542) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.345 Fit side-chains REVERT: A 226 MET cc_start: 0.8910 (mtm) cc_final: 0.8642 (mtp) REVERT: A 240 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7378 (pp) REVERT: A 313 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8241 (mt-10) REVERT: Y 42 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7675 (tt0) REVERT: Y 161 LEU cc_start: 0.9251 (mp) cc_final: 0.9044 (mp) REVERT: Y 226 MET cc_start: 0.8928 (mtm) cc_final: 0.8657 (mtp) REVERT: Y 240 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7357 (pp) REVERT: Y 313 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8261 (mt-10) outliers start: 11 outliers final: 5 residues processed: 84 average time/residue: 1.3584 time to fit residues: 119.7186 Evaluate side-chains 85 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 240 LEU Chi-restraints excluded: chain Y residue 250 LEU Chi-restraints excluded: chain Y residue 313 GLU Chi-restraints excluded: chain Y residue 421 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 34 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.097618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.085773 restraints weight = 33546.167| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.51 r_work: 0.2918 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6840 Z= 0.150 Angle : 0.539 10.312 9326 Z= 0.275 Chirality : 0.077 1.661 1158 Planarity : 0.004 0.057 1128 Dihedral : 4.372 23.060 908 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.56 % Allowed : 11.51 % Favored : 86.93 % 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: 1.77 (0.29), residues: 886 helix: 2.04 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -2.95 (0.42), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG Y 252 TYR 0.003 0.001 TYR A 237 PHE 0.010 0.001 PHE Y 277 TRP 0.013 0.002 TRP A 311 HIS 0.003 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6840) covalent geometry : angle 0.53913 ( 9326) hydrogen bonds : bond 0.04027 ( 516) hydrogen bonds : angle 4.22850 ( 1542) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.320 Fit side-chains REVERT: A 240 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7350 (pp) REVERT: A 313 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8260 (mt-10) REVERT: A 362 ILE cc_start: 0.8765 (pt) cc_final: 0.8506 (mt) REVERT: Y 42 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: Y 240 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7349 (pp) REVERT: Y 313 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8267 (mt-10) REVERT: Y 362 ILE cc_start: 0.8773 (pt) cc_final: 0.8490 (mt) outliers start: 11 outliers final: 6 residues processed: 83 average time/residue: 1.3900 time to fit residues: 120.9338 Evaluate side-chains 85 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 240 LEU Chi-restraints excluded: chain Y residue 250 LEU Chi-restraints excluded: chain Y residue 313 GLU Chi-restraints excluded: chain Y residue 355 HIS Chi-restraints excluded: chain Y residue 421 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 47 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 0.0770 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.098014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.086563 restraints weight = 33130.490| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.46 r_work: 0.2963 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6840 Z= 0.111 Angle : 0.524 10.441 9326 Z= 0.263 Chirality : 0.077 1.662 1158 Planarity : 0.004 0.057 1128 Dihedral : 4.333 23.477 908 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.56 % Allowed : 11.93 % Favored : 86.51 % 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: 1.89 (0.30), residues: 886 helix: 2.15 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -3.00 (0.41), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 252 TYR 0.004 0.001 TYR A 36 PHE 0.007 0.001 PHE A 277 TRP 0.012 0.001 TRP Y 311 HIS 0.003 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6840) covalent geometry : angle 0.52352 ( 9326) hydrogen bonds : bond 0.03770 ( 516) hydrogen bonds : angle 4.17289 ( 1542) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.304 Fit side-chains REVERT: A 226 MET cc_start: 0.8905 (mtm) cc_final: 0.8608 (mtp) REVERT: A 240 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7372 (pp) REVERT: A 313 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8259 (mt-10) REVERT: Y 42 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7681 (tt0) REVERT: Y 161 LEU cc_start: 0.9238 (mp) cc_final: 0.9025 (mp) REVERT: Y 226 MET cc_start: 0.8922 (mtm) cc_final: 0.8624 (mtp) REVERT: Y 240 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7363 (pp) REVERT: Y 313 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8274 (mt-10) outliers start: 11 outliers final: 5 residues processed: 84 average time/residue: 1.3842 time to fit residues: 122.0596 Evaluate side-chains 85 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 240 LEU Chi-restraints excluded: chain Y residue 250 LEU Chi-restraints excluded: chain Y residue 313 GLU Chi-restraints excluded: chain Y residue 355 HIS Chi-restraints excluded: chain Y residue 421 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN Y 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.095470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.083904 restraints weight = 33708.567| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.47 r_work: 0.2921 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6840 Z= 0.187 Angle : 0.560 10.298 9326 Z= 0.289 Chirality : 0.078 1.662 1158 Planarity : 0.005 0.056 1128 Dihedral : 4.397 22.699 908 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.42 % Allowed : 11.93 % Favored : 86.65 % 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: 1.71 (0.29), residues: 886 helix: 1.99 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -2.95 (0.42), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 307 TYR 0.004 0.001 TYR A 237 PHE 0.012 0.001 PHE Y 277 TRP 0.013 0.002 TRP A 311 HIS 0.003 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 6840) covalent geometry : angle 0.55982 ( 9326) hydrogen bonds : bond 0.04212 ( 516) hydrogen bonds : angle 4.27881 ( 1542) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3866.27 seconds wall clock time: 65 minutes 59.31 seconds (3959.31 seconds total)