Starting phenix.real_space_refine on Sat Aug 23 16:50:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wu3_21904/08_2025/6wu3_21904_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wu3_21904/08_2025/6wu3_21904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wu3_21904/08_2025/6wu3_21904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wu3_21904/08_2025/6wu3_21904.map" model { file = "/net/cci-nas-00/data/ceres_data/6wu3_21904/08_2025/6wu3_21904_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wu3_21904/08_2025/6wu3_21904_neut.cif" } resolution = 3.16 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: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 4450 2.51 5 N 1044 2.21 5 O 1128 1.98 5 H 6936 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13610 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6805 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 6805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6805 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.32, per 1000 atoms: 0.17 Number of scatterers: 13610 At special positions: 0 Unit cell: (90.789, 97.641, 76.514, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1128 8.00 N 1044 7.00 C 4450 6.00 H 6936 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: 0.79 Conformation dependent library (CDL) restraints added in 257.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 19 through 38 removed outlier: 3.596A pdb=" N LEU A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) 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 113 removed outlier: 3.795A pdb=" N PHE A 98 " --> pdb=" O ASN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.521A pdb=" N ALA A 127 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 147 Processing helix chain 'A' and resid 151 through 167 removed outlier: 3.796A 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: 4.021A pdb=" N TYR A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.907A pdb=" N ALA A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 240 removed outlier: 4.372A 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 306 Processing helix chain 'A' and resid 310 through 318 Processing helix chain 'A' and resid 319 through 339 removed outlier: 3.680A pdb=" N LEU A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 356 removed outlier: 5.003A pdb=" N ASP A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N MET A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 356 " --> pdb=" O MET A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 373 Processing helix chain 'A' and resid 377 through 392 Proline residue: A 387 - end of helix Processing helix chain 'A' and resid 401 through 413 removed outlier: 3.754A pdb=" N SER A 412 " --> pdb=" O ALA A 408 " (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 460 Processing helix chain 'C' and resid 19 through 38 removed outlier: 3.596A pdb=" N LEU C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 62 Processing helix chain 'C' and resid 65 through 79 Proline residue: C 74 - end of helix Processing helix chain 'C' and resid 84 through 90 Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.795A pdb=" N PHE C 98 " --> pdb=" O ASN C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 127 removed outlier: 3.522A pdb=" N ALA C 127 " --> pdb=" O VAL C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 147 Processing helix chain 'C' and resid 151 through 167 removed outlier: 3.797A pdb=" N ALA C 155 " --> pdb=" O ASN C 151 " (cutoff:3.500A) Proline residue: C 160 - end of helix Processing helix chain 'C' and resid 174 through 193 removed outlier: 4.022A pdb=" N TYR C 178 " --> pdb=" O GLN C 174 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 211 removed outlier: 3.906A pdb=" N ALA C 204 " --> pdb=" O SER C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 240 removed outlier: 4.372A pdb=" N PHE C 220 " --> pdb=" O ASP C 216 " (cutoff:3.500A) Proline residue: C 223 - end of helix Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 260 through 277 Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 290 through 306 Processing helix chain 'C' and resid 310 through 318 Processing helix chain 'C' and resid 319 through 339 removed outlier: 3.679A pdb=" N LEU C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 356 removed outlier: 5.003A pdb=" N ASP C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N MET C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET C 356 " --> pdb=" O MET C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 373 Processing helix chain 'C' and resid 377 through 392 Proline residue: C 387 - end of helix Processing helix chain 'C' and resid 401 through 413 removed outlier: 3.754A pdb=" N SER C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 Processing helix chain 'C' and resid 421 through 429 Processing helix chain 'C' and resid 434 through 460 490 hydrogen bonds defined for protein. 1464 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: 2.90 Time building geometry restraints manager: 1.10 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: 6930 1.03 - 1.22: 6 1.22 - 1.42: 2757 1.42 - 1.61: 3977 1.61 - 1.80: 98 Bond restraints: 13768 Sorted by residual: bond pdb=" CG LEU A 197 " pdb=" CD1 LEU A 197 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.33e+00 bond pdb=" CG LEU C 197 " pdb=" CD1 LEU C 197 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.33e+00 bond pdb=" CG LEU A 301 " pdb=" CD2 LEU A 301 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CG LEU C 301 " pdb=" CD2 LEU C 301 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 bond pdb=" CG1 ILE A 71 " pdb=" CD1 ILE A 71 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.14e+00 ... (remaining 13763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 22766 1.00 - 2.00: 2106 2.00 - 3.00: 106 3.00 - 4.00: 34 4.00 - 5.00: 12 Bond angle restraints: 25024 Sorted by residual: angle pdb=" N VAL A 401 " pdb=" CA VAL A 401 " pdb=" C VAL A 401 " ideal model delta sigma weight residual 112.96 109.12 3.84 1.00e+00 1.00e+00 1.47e+01 angle pdb=" N VAL C 401 " pdb=" CA VAL C 401 " pdb=" C VAL C 401 " ideal model delta sigma weight residual 112.96 109.14 3.82 1.00e+00 1.00e+00 1.46e+01 angle pdb=" CA VAL A 401 " pdb=" C VAL A 401 " pdb=" N LEU A 402 " ideal model delta sigma weight residual 118.65 115.98 2.67 1.07e+00 8.73e-01 6.23e+00 angle pdb=" CA VAL C 401 " pdb=" C VAL C 401 " pdb=" N LEU C 402 " ideal model delta sigma weight residual 118.65 116.02 2.63 1.07e+00 8.73e-01 6.04e+00 angle pdb=" CG LYS A 259 " pdb=" CD LYS A 259 " pdb=" CE LYS A 259 " ideal model delta sigma weight residual 111.30 116.30 -5.00 2.30e+00 1.89e-01 4.72e+00 ... (remaining 25019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 5567 17.32 - 34.63: 569 34.63 - 51.95: 214 51.95 - 69.26: 87 69.26 - 86.58: 23 Dihedral angle restraints: 6460 sinusoidal: 3384 harmonic: 3076 Sorted by residual: dihedral pdb=" CA PHE C 83 " pdb=" C PHE C 83 " pdb=" N GLU C 84 " pdb=" CA GLU C 84 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA PHE A 83 " pdb=" C PHE A 83 " pdb=" N GLU A 84 " pdb=" CA GLU A 84 " ideal model delta harmonic sigma weight residual 180.00 162.06 17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA PHE C 80 " pdb=" C PHE C 80 " pdb=" N GLY C 81 " pdb=" CA GLY C 81 " ideal model delta harmonic sigma weight residual 180.00 164.11 15.89 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 6457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 575 0.024 - 0.048: 302 0.048 - 0.072: 209 0.072 - 0.097: 59 0.097 - 0.121: 13 Chirality restraints: 1158 Sorted by residual: chirality pdb=" CA PRO C 418 " pdb=" N PRO C 418 " pdb=" C PRO C 418 " pdb=" CB PRO C 418 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.64e-01 chirality pdb=" CA PRO A 418 " pdb=" N PRO A 418 " pdb=" C PRO A 418 " pdb=" CB PRO A 418 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.60e-01 chirality pdb=" CA ILE C 433 " pdb=" N ILE C 433 " pdb=" C ILE C 433 " pdb=" CB ILE C 433 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.21e-01 ... (remaining 1155 not shown) Planarity restraints: 1986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 421 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A 422 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 422 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 422 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 421 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.22e+00 pdb=" N PRO C 422 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 422 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 422 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 159 " -0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO C 160 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 160 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 160 " -0.017 5.00e-02 4.00e+02 ... (remaining 1983 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 729 2.16 - 2.77: 27577 2.77 - 3.38: 39437 3.38 - 3.99: 50104 3.99 - 4.60: 80706 Nonbonded interactions: 198553 Sorted by model distance: nonbonded pdb=" O GLY A 184 " pdb=" HG SER A 188 " model vdw 1.555 2.450 nonbonded pdb=" O GLY C 184 " pdb=" HG SER C 188 " model vdw 1.575 2.450 nonbonded pdb=" O VAL C 57 " pdb=" HG1 THR C 61 " model vdw 1.607 2.450 nonbonded pdb=" O PRO C 387 " pdb=" HG1 THR C 391 " model vdw 1.611 2.450 nonbonded pdb=" O ILE C 267 " pdb=" HG1 THR C 271 " model vdw 1.614 2.450 ... (remaining 198548 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 'C' } 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: 4.290 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: 0.040 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.840 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 : 0.008 0.042 6832 Z= 0.310 Angle : 0.603 4.997 9318 Z= 0.341 Chirality : 0.039 0.121 1158 Planarity : 0.004 0.037 1128 Dihedral : 15.887 84.129 2292 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 6.27 % Allowed : 14.96 % Favored : 78.77 % 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 aren not related in a simple way. whole: -3.62 (0.23), residues: 886 helix: -1.65 (0.16), residues: 696 sheet: None (None), residues: 0 loop : -4.72 (0.31), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 252 TYR 0.008 0.001 TYR C 36 PHE 0.014 0.001 PHE C 98 TRP 0.006 0.001 TRP C 311 HIS 0.003 0.001 HIS C 432 Details of bonding type rmsd covalent geometry : bond 0.00763 ( 6832) covalent geometry : angle 0.60286 ( 9318) hydrogen bonds : bond 0.13435 ( 490) hydrogen bonds : angle 5.82696 ( 1464) *********************** 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 LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.6682 (ptpp) REVERT: A 216 ASP cc_start: 0.7898 (t0) cc_final: 0.7649 (t0) REVERT: C 173 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6628 (ptpp) REVERT: C 216 ASP cc_start: 0.7867 (t0) cc_final: 0.7650 (t0) outliers start: 44 outliers final: 34 residues processed: 183 average time/residue: 0.1563 time to fit residues: 38.6243 Evaluate side-chains 164 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 454 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN C 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.129165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.104281 restraints weight = 26959.678| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.35 r_work: 0.3069 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6832 Z= 0.140 Angle : 0.569 4.931 9318 Z= 0.301 Chirality : 0.035 0.132 1158 Planarity : 0.004 0.034 1128 Dihedral : 9.081 59.513 960 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.85 % Allowed : 17.09 % Favored : 79.06 % 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 aren not related in a simple way. whole: -1.46 (0.27), residues: 886 helix: -0.04 (0.19), residues: 704 sheet: None (None), residues: 0 loop : -4.53 (0.36), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 20 TYR 0.007 0.001 TYR C 36 PHE 0.014 0.001 PHE A 273 TRP 0.012 0.001 TRP A 311 HIS 0.003 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6832) covalent geometry : angle 0.56908 ( 9318) hydrogen bonds : bond 0.04267 ( 490) hydrogen bonds : angle 4.35575 ( 1464) *********************** 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 LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.6995 (ptpp) REVERT: A 216 ASP cc_start: 0.8546 (t0) cc_final: 0.8332 (t0) REVERT: A 439 MET cc_start: 0.7913 (mtm) cc_final: 0.7598 (mtt) REVERT: C 173 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.6911 (ptpp) REVERT: C 216 ASP cc_start: 0.8554 (t0) cc_final: 0.8328 (t0) outliers start: 27 outliers final: 22 residues processed: 153 average time/residue: 0.1283 time to fit residues: 28.6747 Evaluate side-chains 156 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 454 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 86 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN C 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.101166 restraints weight = 27497.752| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.32 r_work: 0.3032 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6832 Z= 0.123 Angle : 0.524 6.233 9318 Z= 0.275 Chirality : 0.034 0.122 1158 Planarity : 0.004 0.033 1128 Dihedral : 8.464 58.111 941 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.99 % Allowed : 18.80 % Favored : 77.21 % 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 aren not related in a simple way. whole: -0.52 (0.29), residues: 886 helix: 0.61 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -4.24 (0.38), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 440 TYR 0.006 0.001 TYR C 36 PHE 0.018 0.001 PHE A 54 TRP 0.011 0.001 TRP A 311 HIS 0.004 0.001 HIS C 19 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 6832) covalent geometry : angle 0.52406 ( 9318) hydrogen bonds : bond 0.03841 ( 490) hydrogen bonds : angle 4.14020 ( 1464) *********************** 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 LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7017 (ptpp) REVERT: A 216 ASP cc_start: 0.8592 (t0) cc_final: 0.8378 (m-30) REVERT: A 307 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7815 (mtm110) REVERT: A 439 MET cc_start: 0.7925 (mtm) cc_final: 0.7604 (mtt) REVERT: C 19 HIS cc_start: 0.8093 (t70) cc_final: 0.7699 (t-90) REVERT: C 62 GLU cc_start: 0.8204 (tt0) cc_final: 0.7830 (tp30) REVERT: C 173 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.6947 (ptpp) REVERT: C 210 VAL cc_start: 0.9261 (m) cc_final: 0.9036 (p) REVERT: C 216 ASP cc_start: 0.8601 (t0) cc_final: 0.8387 (m-30) outliers start: 28 outliers final: 23 residues processed: 159 average time/residue: 0.1394 time to fit residues: 30.8050 Evaluate side-chains 157 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 454 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.119358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.094579 restraints weight = 27895.115| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.32 r_work: 0.2773 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6832 Z= 0.183 Angle : 0.552 5.246 9318 Z= 0.290 Chirality : 0.035 0.124 1158 Planarity : 0.004 0.037 1128 Dihedral : 8.156 59.730 940 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.13 % Allowed : 18.66 % Favored : 77.21 % 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 aren not related in a simple way. whole: -0.14 (0.29), residues: 886 helix: 0.90 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -4.16 (0.38), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 20 TYR 0.006 0.001 TYR C 36 PHE 0.036 0.001 PHE C 139 TRP 0.012 0.001 TRP A 311 HIS 0.006 0.001 HIS C 19 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 6832) covalent geometry : angle 0.55178 ( 9318) hydrogen bonds : bond 0.03857 ( 490) hydrogen bonds : angle 4.17257 ( 1464) *********************** 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 LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7979 (mtm110) REVERT: A 439 MET cc_start: 0.7825 (mtm) cc_final: 0.7500 (mtt) outliers start: 29 outliers final: 26 residues processed: 158 average time/residue: 0.1343 time to fit residues: 30.6891 Evaluate side-chains 157 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 454 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.113746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.088663 restraints weight = 28836.820| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.30 r_work: 0.2845 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6832 Z= 0.239 Angle : 0.580 7.358 9318 Z= 0.307 Chirality : 0.037 0.166 1158 Planarity : 0.004 0.035 1128 Dihedral : 7.557 56.425 932 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.27 % Allowed : 18.66 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.29), residues: 886 helix: 1.03 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -4.20 (0.37), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.006 0.001 TYR C 36 PHE 0.017 0.001 PHE C 98 TRP 0.011 0.001 TRP C 311 HIS 0.004 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00536 ( 6832) covalent geometry : angle 0.58042 ( 9318) hydrogen bonds : bond 0.03981 ( 490) hydrogen bonds : angle 4.29325 ( 1464) *********************** 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 LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 168 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8088 (t-90) cc_final: 0.7755 (t-90) REVERT: C 19 HIS cc_start: 0.8213 (t70) cc_final: 0.7840 (t-90) REVERT: C 173 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7109 (ptpp) outliers start: 30 outliers final: 24 residues processed: 156 average time/residue: 0.1396 time to fit residues: 30.8791 Evaluate side-chains 161 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 454 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 70 optimal weight: 0.0970 chunk 56 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.116870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.091861 restraints weight = 28147.165| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.27 r_work: 0.2899 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6832 Z= 0.116 Angle : 0.524 4.911 9318 Z= 0.272 Chirality : 0.034 0.132 1158 Planarity : 0.004 0.035 1128 Dihedral : 6.838 54.582 927 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.85 % Allowed : 19.94 % Favored : 76.21 % 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 aren not related in a simple way. whole: 0.49 (0.29), residues: 886 helix: 1.35 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -4.04 (0.38), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 307 TYR 0.004 0.001 TYR C 36 PHE 0.028 0.001 PHE A 139 TRP 0.013 0.001 TRP C 311 HIS 0.004 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6832) covalent geometry : angle 0.52404 ( 9318) hydrogen bonds : bond 0.03587 ( 490) hydrogen bonds : angle 3.99078 ( 1464) *********************** 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 LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8043 (t-90) cc_final: 0.7799 (t-90) REVERT: A 173 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7044 (ptpp) REVERT: C 173 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.6908 (ptpp) outliers start: 27 outliers final: 21 residues processed: 160 average time/residue: 0.1380 time to fit residues: 31.2665 Evaluate side-chains 164 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 459 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 49 optimal weight: 0.0870 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.116659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.091882 restraints weight = 28794.481| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.30 r_work: 0.2819 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6832 Z= 0.166 Angle : 0.543 5.520 9318 Z= 0.283 Chirality : 0.035 0.172 1158 Planarity : 0.004 0.035 1128 Dihedral : 6.425 53.506 926 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.42 % Allowed : 20.80 % Favored : 75.78 % 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 aren not related in a simple way. whole: 0.60 (0.29), residues: 886 helix: 1.44 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -4.03 (0.38), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 307 TYR 0.004 0.001 TYR A 178 PHE 0.016 0.001 PHE A 139 TRP 0.011 0.001 TRP C 311 HIS 0.004 0.000 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 6832) covalent geometry : angle 0.54337 ( 9318) hydrogen bonds : bond 0.03658 ( 490) hydrogen bonds : angle 4.05031 ( 1464) *********************** 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 LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8027 (t-90) cc_final: 0.7775 (t-90) REVERT: A 173 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7123 (ptpp) REVERT: C 173 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7042 (ptpp) outliers start: 24 outliers final: 20 residues processed: 149 average time/residue: 0.1346 time to fit residues: 28.0346 Evaluate side-chains 160 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 454 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 85 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 68 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.118470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.093472 restraints weight = 28377.758| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.30 r_work: 0.2906 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6832 Z= 0.114 Angle : 0.521 5.212 9318 Z= 0.269 Chirality : 0.034 0.171 1158 Planarity : 0.003 0.036 1128 Dihedral : 6.152 52.168 925 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.42 % Allowed : 20.80 % Favored : 75.78 % 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 aren not related in a simple way. whole: 0.87 (0.30), residues: 886 helix: 1.59 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -3.71 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 307 TYR 0.004 0.001 TYR A 187 PHE 0.014 0.001 PHE A 139 TRP 0.013 0.001 TRP C 311 HIS 0.005 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 6832) covalent geometry : angle 0.52132 ( 9318) hydrogen bonds : bond 0.03432 ( 490) hydrogen bonds : angle 3.91593 ( 1464) *********************** 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 LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8036 (t-90) cc_final: 0.7798 (t-90) REVERT: A 173 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7066 (ptpp) REVERT: C 173 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.6980 (ptpp) outliers start: 24 outliers final: 21 residues processed: 158 average time/residue: 0.1382 time to fit residues: 30.7215 Evaluate side-chains 166 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 459 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.117098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.091739 restraints weight = 28489.132| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.28 r_work: 0.2882 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6832 Z= 0.129 Angle : 0.524 4.842 9318 Z= 0.271 Chirality : 0.035 0.185 1158 Planarity : 0.003 0.036 1128 Dihedral : 6.002 51.796 925 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.42 % Allowed : 21.08 % Favored : 75.50 % 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 aren not related in a simple way. whole: 0.95 (0.30), residues: 886 helix: 1.63 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -3.63 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 307 TYR 0.003 0.001 TYR C 36 PHE 0.011 0.001 PHE A 139 TRP 0.012 0.001 TRP A 311 HIS 0.007 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6832) covalent geometry : angle 0.52382 ( 9318) hydrogen bonds : bond 0.03446 ( 490) hydrogen bonds : angle 3.91814 ( 1464) *********************** 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 LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8069 (t-90) cc_final: 0.7830 (t-90) REVERT: A 173 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7137 (ptpp) REVERT: C 173 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7050 (ptpp) outliers start: 24 outliers final: 19 residues processed: 154 average time/residue: 0.1296 time to fit residues: 28.2352 Evaluate side-chains 164 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain C residue 59 TRP Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 459 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 55 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 chunk 84 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3402 r_free = 0.3402 target = 0.117729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.092701 restraints weight = 28136.200| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.26 r_work: 0.2897 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6832 Z= 0.135 Angle : 0.525 5.237 9318 Z= 0.273 Chirality : 0.034 0.181 1158 Planarity : 0.003 0.036 1128 Dihedral : 5.516 51.970 921 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.85 % Allowed : 21.79 % Favored : 75.36 % 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 aren not related in a simple way. whole: 1.02 (0.30), residues: 886 helix: 1.67 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -3.54 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 307 TYR 0.004 0.001 TYR A 178 PHE 0.011 0.001 PHE A 139 TRP 0.011 0.001 TRP C 311 HIS 0.006 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6832) covalent geometry : angle 0.52547 ( 9318) hydrogen bonds : bond 0.03450 ( 490) hydrogen bonds : angle 3.91967 ( 1464) ********************** 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 LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8098 (t-90) cc_final: 0.7876 (t-90) REVERT: A 173 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7092 (ptpp) REVERT: A 439 MET cc_start: 0.7902 (mtm) cc_final: 0.7547 (mtt) REVERT: C 173 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.6986 (ptpp) outliers start: 20 outliers final: 17 residues processed: 157 average time/residue: 0.1292 time to fit residues: 28.9247 Evaluate side-chains 158 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain C residue 59 TRP Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 459 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.115973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.090648 restraints weight = 28801.738| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.28 r_work: 0.2862 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6832 Z= 0.148 Angle : 0.530 4.870 9318 Z= 0.275 Chirality : 0.035 0.182 1158 Planarity : 0.004 0.036 1128 Dihedral : 5.134 51.728 917 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.71 % Allowed : 21.79 % Favored : 75.50 % 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 aren not related in a simple way. whole: 1.05 (0.30), residues: 886 helix: 1.68 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -3.48 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 307 TYR 0.004 0.001 TYR C 178 PHE 0.011 0.001 PHE C 98 TRP 0.011 0.001 TRP C 311 HIS 0.006 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6832) covalent geometry : angle 0.52993 ( 9318) hydrogen bonds : bond 0.03487 ( 490) hydrogen bonds : angle 3.93618 ( 1464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2985.46 seconds wall clock time: 51 minutes 14.09 seconds (3074.09 seconds total)