Starting phenix.real_space_refine on Thu Jun 12 01:36:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t9g_25757/06_2025/7t9g_25757.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9g_25757/06_2025/7t9g_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_25757/06_2025/7t9g_25757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9g_25757/06_2025/7t9g_25757.map" model { file = "/net/cci-nas-00/data/ceres_data/7t9g_25757/06_2025/7t9g_25757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9g_25757/06_2025/7t9g_25757.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.16, per 1000 atoms: 0.67 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: 4.43 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.12 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: 8.55 Time building geometry restraints manager: 5.51 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: 0.04 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: 55.480 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: 0.220 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 43.820 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:120.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 221.570 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.001 TRP A 461 HIS 0.007 0.001 HIS A 355 PHE 0.018 0.001 PHE A 100 TYR 0.005 0.001 TYR A 36 ARG 0.001 0.000 ARG A 175 Details of bonding type rmsd hydrogen bonds : bond 0.08354 ( 516) hydrogen bonds : angle 5.46481 ( 1542) covalent geometry : bond 0.00268 ( 6840) covalent geometry : angle 0.55041 ( 9326) *********************** 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 : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 101 average time/residue: 2.9975 time to fit residues: 321.8568 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 : 1.636 ------------------------------------------------------------------------------- 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 74 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3349 r_free = 0.3349 target = 0.104729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.092885 restraints weight = 31755.005| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.47 r_work: 0.3056 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1028 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= 0.136 Angle : 0.557 10.736 9326 Z= 0.284 Chirality : 0.077 1.667 1158 Planarity : 0.005 0.057 1128 Dihedral : 4.838 44.070 914 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.85 % Allowed : 6.53 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.30), residues: 886 helix: 1.92 (0.20), residues: 716 sheet: None (None), residues: 0 loop : -2.90 (0.41), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 217 HIS 0.003 0.001 HIS Y 310 PHE 0.013 0.001 PHE Y 277 TYR 0.005 0.001 TYR A 36 ARG 0.004 0.001 ARG Y 20 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 516) hydrogen bonds : angle 4.42844 ( 1542) covalent geometry : bond 0.00302 ( 6840) covalent geometry : angle 0.55663 ( 9326) *********************** 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 95 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8021 (pp) REVERT: Y 20 ARG cc_start: 0.7363 (ttp-110) cc_final: 0.7122 (ttt180) REVERT: Y 240 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.7477 (pp) outliers start: 13 outliers final: 3 residues processed: 90 average time/residue: 2.6331 time to fit residues: 252.1519 Evaluate side-chains 84 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 355 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 11 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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 = 0.3233 r_free = 0.3233 target = 0.096522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.084888 restraints weight = 32837.210| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.43 r_work: 0.2931 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6840 Z= 0.200 Angle : 0.577 10.212 9326 Z= 0.299 Chirality : 0.078 1.679 1158 Planarity : 0.005 0.056 1128 Dihedral : 4.487 22.327 908 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.85 % Allowed : 8.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.29), residues: 886 helix: 1.81 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -3.06 (0.41), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Y 311 HIS 0.003 0.001 HIS Y 43 PHE 0.014 0.001 PHE Y 277 TYR 0.004 0.001 TYR A 237 ARG 0.004 0.001 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 516) hydrogen bonds : angle 4.48247 ( 1542) covalent geometry : bond 0.00456 ( 6840) covalent geometry : angle 0.57719 ( 9326) *********************** 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 91 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 1.569 Fit side-chains REVERT: A 226 MET cc_start: 0.8893 (mtm) cc_final: 0.8644 (mtp) REVERT: A 240 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.7429 (pp) REVERT: A 313 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8329 (mt-10) REVERT: Y 20 ARG cc_start: 0.7579 (ttp-110) cc_final: 0.7295 (ttt180) REVERT: Y 226 MET cc_start: 0.8896 (mtm) cc_final: 0.8647 (mtp) REVERT: Y 240 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.7456 (pp) REVERT: Y 313 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8380 (mt-10) outliers start: 13 outliers final: 4 residues processed: 86 average time/residue: 2.8114 time to fit residues: 257.3158 Evaluate side-chains 80 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 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 30 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 = 0.3236 r_free = 0.3236 target = 0.096815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.085234 restraints weight = 33007.228| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.45 r_work: 0.2937 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.2235 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= 0.168 Angle : 0.552 10.396 9326 Z= 0.284 Chirality : 0.077 1.658 1158 Planarity : 0.005 0.061 1128 Dihedral : 4.472 23.004 908 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.70 % Allowed : 8.95 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.29), residues: 886 helix: 1.85 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -3.04 (0.41), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Y 311 HIS 0.004 0.001 HIS A 65 PHE 0.011 0.001 PHE Y 277 TYR 0.004 0.001 TYR A 36 ARG 0.002 0.000 ARG A 175 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 516) hydrogen bonds : angle 4.36807 ( 1542) covalent geometry : bond 0.00383 ( 6840) covalent geometry : angle 0.55161 ( 9326) *********************** 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 85 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 1.017 Fit side-chains REVERT: A 240 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7422 (pp) REVERT: Y 20 ARG cc_start: 0.7564 (ttp-110) cc_final: 0.7285 (ttt180) REVERT: Y 240 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.7419 (pp) outliers start: 12 outliers final: 7 residues processed: 80 average time/residue: 2.7674 time to fit residues: 233.1986 Evaluate side-chains 82 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 356 MET 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 421 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 0.0070 chunk 17 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- 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 = 0.3238 r_free = 0.3238 target = 0.096886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.085274 restraints weight = 33334.449| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.46 r_work: 0.2942 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6840 Z= 0.150 Angle : 0.542 10.324 9326 Z= 0.277 Chirality : 0.077 1.661 1158 Planarity : 0.004 0.060 1128 Dihedral : 4.425 23.017 908 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.70 % Allowed : 10.23 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.29), residues: 886 helix: 1.92 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -3.05 (0.40), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 311 HIS 0.004 0.001 HIS A 65 PHE 0.010 0.001 PHE A 277 TYR 0.004 0.001 TYR A 36 ARG 0.002 0.000 ARG Y 307 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 516) hydrogen bonds : angle 4.33541 ( 1542) covalent geometry : bond 0.00340 ( 6840) covalent geometry : angle 0.54169 ( 9326) *********************** 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 86 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.981 Fit side-chains REVERT: A 226 MET cc_start: 0.8928 (mtm) cc_final: 0.8668 (mtp) REVERT: A 240 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.7416 (pp) REVERT: A 313 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8292 (mt-10) REVERT: Y 20 ARG cc_start: 0.7595 (ttp-110) cc_final: 0.7359 (ttt180) REVERT: Y 226 MET cc_start: 0.8928 (mtm) cc_final: 0.8666 (mtp) REVERT: Y 240 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.7430 (pp) REVERT: Y 313 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8297 (mt-10) outliers start: 12 outliers final: 6 residues processed: 82 average time/residue: 2.7706 time to fit residues: 239.0884 Evaluate side-chains 82 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 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 69 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 84 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3257 r_free = 0.3257 target = 0.098218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.086663 restraints weight = 33615.697| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.46 r_work: 0.2959 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2433 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 10.436 9326 Z= 0.264 Chirality : 0.077 1.662 1158 Planarity : 0.004 0.059 1128 Dihedral : 4.363 23.391 908 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.28 % Allowed : 10.65 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.30), residues: 886 helix: 2.10 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -3.02 (0.41), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 311 HIS 0.003 0.001 HIS Y 65 PHE 0.007 0.001 PHE Y 54 TYR 0.004 0.001 TYR Y 36 ARG 0.002 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 516) hydrogen bonds : angle 4.22282 ( 1542) covalent geometry : bond 0.00248 ( 6840) covalent geometry : angle 0.52431 ( 9326) *********************** 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 83 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 1.120 Fit side-chains REVERT: A 226 MET cc_start: 0.8945 (mtm) cc_final: 0.8685 (mtp) REVERT: A 240 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.7420 (pp) REVERT: Y 226 MET cc_start: 0.8934 (mtm) cc_final: 0.8674 (mtp) REVERT: Y 240 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7421 (pp) REVERT: Y 313 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8262 (mt-10) outliers start: 9 outliers final: 6 residues processed: 81 average time/residue: 2.8227 time to fit residues: 240.6486 Evaluate side-chains 81 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 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 2 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3208 r_free = 0.3208 target = 0.095051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.083455 restraints weight = 33813.172| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.48 r_work: 0.2912 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6840 Z= 0.210 Angle : 0.572 10.241 9326 Z= 0.297 Chirality : 0.078 1.662 1158 Planarity : 0.005 0.058 1128 Dihedral : 4.471 22.524 908 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.56 % Allowed : 11.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.29), residues: 886 helix: 1.89 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -2.96 (0.42), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Y 311 HIS 0.003 0.001 HIS A 43 PHE 0.014 0.001 PHE Y 277 TYR 0.004 0.001 TYR Y 237 ARG 0.001 0.000 ARG A 440 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 516) hydrogen bonds : angle 4.34202 ( 1542) covalent geometry : bond 0.00481 ( 6840) covalent geometry : angle 0.57204 ( 9326) *********************** 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 86 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.971 Fit side-chains REVERT: A 240 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7345 (pp) REVERT: A 313 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8280 (mt-10) REVERT: A 362 ILE cc_start: 0.8801 (pt) cc_final: 0.8549 (mt) REVERT: Y 240 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7355 (pp) REVERT: Y 313 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8351 (mt-10) REVERT: Y 362 ILE cc_start: 0.8797 (pt) cc_final: 0.8548 (mt) outliers start: 11 outliers final: 6 residues processed: 84 average time/residue: 2.9060 time to fit residues: 256.4115 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 : 1.126 ------------------------------------------------------------------------------- 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 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 9 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3228 r_free = 0.3228 target = 0.096441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.084893 restraints weight = 33542.280| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.47 r_work: 0.2935 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2690 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= 0.147 Angle : 0.544 10.334 9326 Z= 0.278 Chirality : 0.077 1.659 1158 Planarity : 0.004 0.059 1128 Dihedral : 4.429 23.031 908 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.42 % Allowed : 12.50 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.29), residues: 886 helix: 1.98 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -2.99 (0.41), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Y 311 HIS 0.002 0.001 HIS A 65 PHE 0.010 0.001 PHE Y 277 TYR 0.004 0.001 TYR Y 36 ARG 0.002 0.000 ARG Y 252 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 516) hydrogen bonds : angle 4.30276 ( 1542) covalent geometry : bond 0.00333 ( 6840) covalent geometry : angle 0.54377 ( 9326) *********************** 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 84 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 1.004 Fit side-chains REVERT: A 226 MET cc_start: 0.8923 (mtm) cc_final: 0.8629 (mtp) REVERT: A 240 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7351 (pp) REVERT: A 313 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8290 (mt-10) REVERT: Y 226 MET cc_start: 0.8926 (mtm) cc_final: 0.8633 (mtp) REVERT: Y 240 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7345 (pp) REVERT: Y 313 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8304 (mt-10) outliers start: 10 outliers final: 5 residues processed: 82 average time/residue: 2.8383 time to fit residues: 245.0007 Evaluate side-chains 81 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 50 optimal weight: 0.0570 chunk 37 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.8700 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.097741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.086232 restraints weight = 32948.730| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.45 r_work: 0.2961 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2697 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= 0.118 Angle : 0.531 10.423 9326 Z= 0.268 Chirality : 0.077 1.662 1158 Planarity : 0.004 0.058 1128 Dihedral : 4.368 23.031 908 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.28 % Allowed : 12.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.30), residues: 886 helix: 2.10 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -2.97 (0.41), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 311 HIS 0.003 0.001 HIS A 65 PHE 0.007 0.001 PHE Y 54 TYR 0.004 0.001 TYR A 36 ARG 0.002 0.001 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 516) hydrogen bonds : angle 4.22648 ( 1542) covalent geometry : bond 0.00264 ( 6840) covalent geometry : angle 0.53069 ( 9326) *********************** 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 83 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 1.392 Fit side-chains REVERT: A 226 MET cc_start: 0.8910 (mtm) cc_final: 0.8611 (mtp) REVERT: A 240 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7377 (pp) REVERT: A 313 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8296 (mt-10) REVERT: Y 226 MET cc_start: 0.8913 (mtm) cc_final: 0.8614 (mtp) REVERT: Y 240 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7372 (pp) REVERT: Y 313 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8296 (mt-10) outliers start: 9 outliers final: 4 residues processed: 82 average time/residue: 3.2867 time to fit residues: 285.0284 Evaluate side-chains 80 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 2.410 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 59 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3224 r_free = 0.3224 target = 0.096108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.084544 restraints weight = 33493.228| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.47 r_work: 0.2932 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.2791 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= 0.173 Angle : 0.550 10.348 9326 Z= 0.282 Chirality : 0.078 1.664 1158 Planarity : 0.004 0.058 1128 Dihedral : 4.382 22.398 908 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.42 % Allowed : 12.36 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.29), residues: 886 helix: 2.00 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -2.93 (0.41), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Y 311 HIS 0.003 0.001 HIS A 65 PHE 0.011 0.001 PHE Y 277 TYR 0.003 0.001 TYR A 237 ARG 0.002 0.001 ARG Y 252 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 516) hydrogen bonds : angle 4.28745 ( 1542) covalent geometry : bond 0.00395 ( 6840) covalent geometry : angle 0.55003 ( 9326) ********************** 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 82 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 1.207 Fit side-chains REVERT: A 226 MET cc_start: 0.8911 (mtm) cc_final: 0.8639 (mtp) REVERT: A 240 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7353 (pp) REVERT: A 313 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8295 (mt-10) REVERT: A 362 ILE cc_start: 0.8797 (pt) cc_final: 0.8509 (mt) REVERT: Y 226 MET cc_start: 0.8917 (mtm) cc_final: 0.8647 (mtp) REVERT: Y 240 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7343 (pp) REVERT: Y 313 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8341 (mt-10) REVERT: Y 362 ILE cc_start: 0.8792 (pt) cc_final: 0.8505 (mt) outliers start: 10 outliers final: 6 residues processed: 80 average time/residue: 3.8362 time to fit residues: 324.9854 Evaluate side-chains 82 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 1.501 ------------------------------------------------------------------------------- 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 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 46 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.3245 r_free = 0.3245 target = 0.097521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.085962 restraints weight = 33402.987| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.47 r_work: 0.2954 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.2798 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= 0.124 Angle : 0.532 10.430 9326 Z= 0.270 Chirality : 0.077 1.661 1158 Planarity : 0.004 0.058 1128 Dihedral : 4.363 23.049 908 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.28 % Allowed : 12.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.29), residues: 886 helix: 2.08 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -2.92 (0.41), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 311 HIS 0.003 0.001 HIS A 65 PHE 0.008 0.001 PHE Y 277 TYR 0.003 0.001 TYR Y 36 ARG 0.002 0.000 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 516) hydrogen bonds : angle 4.23367 ( 1542) covalent geometry : bond 0.00279 ( 6840) covalent geometry : angle 0.53175 ( 9326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10360.79 seconds wall clock time: 186 minutes 33.63 seconds (11193.63 seconds total)