Starting phenix.real_space_refine on Thu Jul 2 05:24:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wpy_66153/07_2026/9wpy_66153.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wpy_66153/07_2026/9wpy_66153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wpy_66153/07_2026/9wpy_66153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wpy_66153/07_2026/9wpy_66153.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wpy_66153/07_2026/9wpy_66153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wpy_66153/07_2026/9wpy_66153.map" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.069 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 P 6 5.49 5 S 56 5.16 5 C 4630 2.51 5 N 978 2.21 5 O 1110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6780 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2542 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 19, 'TRANS': 307} Chain: "B" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 426 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "C" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2542 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 19, 'TRANS': 307} Chain: "D" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 426 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "A" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 394 Unusual residues: {'CLR': 4, 'PLM': 7, 'POV': 3, 'ZWY': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PLM:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 394 Unusual residues: {'CLR': 4, 'PLM': 7, 'POV': 3, 'ZWY': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PLM:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.80, per 1000 atoms: 0.27 Number of scatterers: 6780 At special positions: 0 Unit cell: (91.3, 89.1, 94.6, 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 56 16.00 P 6 15.00 O 1110 8.00 N 978 7.00 C 4630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 284 " distance=2.03 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=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 394.7 milliseconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1436 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 75.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 15 through 25 Processing helix chain 'A' and resid 38 through 44 removed outlier: 3.649A pdb=" N ARG A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 78 Processing helix chain 'A' and resid 81 through 92 removed outlier: 3.638A pdb=" N THR A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 108 Processing helix chain 'A' and resid 111 through 139 removed outlier: 4.297A pdb=" N TYR A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 173 through 202 Proline residue: A 184 - end of helix removed outlier: 3.897A pdb=" N TYR A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 247 removed outlier: 3.894A pdb=" N TRP A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 280 removed outlier: 4.191A pdb=" N GLN A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 289 through 318 removed outlier: 3.885A pdb=" N LEU A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 28 Processing helix chain 'B' and resid 33 through 68 Processing helix chain 'C' and resid 15 through 25 Processing helix chain 'C' and resid 38 through 44 removed outlier: 3.649A pdb=" N ARG C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 78 Processing helix chain 'C' and resid 81 through 92 removed outlier: 3.637A pdb=" N THR C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 108 Processing helix chain 'C' and resid 111 through 139 removed outlier: 4.297A pdb=" N TYR C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 148 Processing helix chain 'C' and resid 173 through 202 Proline residue: C 184 - end of helix removed outlier: 3.897A pdb=" N TYR C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 247 removed outlier: 3.895A pdb=" N TRP C 220 " --> pdb=" O SER C 216 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 280 removed outlier: 4.191A pdb=" N GLN C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 289 through 318 removed outlier: 3.885A pdb=" N LEU C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 318 " --> pdb=" O ARG C 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 33 through 68 438 hydrogen bonds defined for protein. 1314 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: 0.81 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1009 1.33 - 1.45: 1543 1.45 - 1.57: 4280 1.57 - 1.69: 12 1.69 - 1.81: 80 Bond restraints: 6924 Sorted by residual: bond pdb=" O20 ZWY C 415 " pdb=" S21 ZWY C 415 " ideal model delta sigma weight residual 1.628 1.519 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" O20 ZWY A 414 " pdb=" S21 ZWY A 414 " ideal model delta sigma weight residual 1.628 1.519 0.109 2.00e-02 2.50e+03 2.94e+01 bond pdb=" O24 ZWY C 415 " pdb=" S21 ZWY C 415 " ideal model delta sigma weight residual 1.460 1.522 -0.062 2.00e-02 2.50e+03 9.58e+00 bond pdb=" O24 ZWY A 414 " pdb=" S21 ZWY A 414 " ideal model delta sigma weight residual 1.460 1.522 -0.062 2.00e-02 2.50e+03 9.56e+00 bond pdb=" N ASP A 204 " pdb=" CA ASP A 204 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.33e-02 5.65e+03 5.89e+00 ... (remaining 6919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 9149 2.45 - 4.89: 137 4.89 - 7.34: 28 7.34 - 9.78: 10 9.78 - 12.23: 4 Bond angle restraints: 9328 Sorted by residual: angle pdb=" CA LEU A 170 " pdb=" CB LEU A 170 " pdb=" CG LEU A 170 " ideal model delta sigma weight residual 116.30 128.53 -12.23 3.50e+00 8.16e-02 1.22e+01 angle pdb=" CA LEU C 170 " pdb=" CB LEU C 170 " pdb=" CG LEU C 170 " ideal model delta sigma weight residual 116.30 128.52 -12.22 3.50e+00 8.16e-02 1.22e+01 angle pdb=" CA ILE B 50 " pdb=" CB ILE B 50 " pdb=" CG1 ILE B 50 " ideal model delta sigma weight residual 110.40 115.95 -5.55 1.70e+00 3.46e-01 1.06e+01 angle pdb=" CA ILE D 50 " pdb=" CB ILE D 50 " pdb=" CG1 ILE D 50 " ideal model delta sigma weight residual 110.40 115.93 -5.53 1.70e+00 3.46e-01 1.06e+01 angle pdb=" O22 ZWY A 414 " pdb=" S21 ZWY A 414 " pdb=" O23 ZWY A 414 " ideal model delta sigma weight residual 113.33 122.96 -9.63 3.00e+00 1.11e-01 1.03e+01 ... (remaining 9323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 4215 16.52 - 33.05: 425 33.05 - 49.57: 158 49.57 - 66.09: 56 66.09 - 82.62: 2 Dihedral angle restraints: 4856 sinusoidal: 2640 harmonic: 2216 Sorted by residual: dihedral pdb=" CG ARG A 85 " pdb=" CD ARG A 85 " pdb=" NE ARG A 85 " pdb=" CZ ARG A 85 " ideal model delta sinusoidal sigma weight residual 90.00 133.62 -43.62 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG C 85 " pdb=" CD ARG C 85 " pdb=" NE ARG C 85 " pdb=" CZ ARG C 85 " ideal model delta sinusoidal sigma weight residual 90.00 133.59 -43.59 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CA TYR C 26 " pdb=" C TYR C 26 " pdb=" N GLY C 27 " pdb=" CA GLY C 27 " ideal model delta harmonic sigma weight residual 180.00 164.35 15.65 0 5.00e+00 4.00e-02 9.80e+00 ... (remaining 4853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1047 0.094 - 0.188: 47 0.188 - 0.282: 0 0.282 - 0.377: 2 0.377 - 0.471: 2 Chirality restraints: 1098 Sorted by residual: chirality pdb=" C07 ZWY A 414 " pdb=" C02 ZWY A 414 " pdb=" C06 ZWY A 414 " pdb=" C08 ZWY A 414 " both_signs ideal model delta sigma weight residual False 2.34 2.81 -0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" C07 ZWY C 415 " pdb=" C02 ZWY C 415 " pdb=" C06 ZWY C 415 " pdb=" C08 ZWY C 415 " both_signs ideal model delta sigma weight residual False 2.34 2.81 -0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" C15 ZWY A 414 " pdb=" C05 ZWY A 414 " pdb=" C14 ZWY A 414 " pdb=" C16 ZWY A 414 " both_signs ideal model delta sigma weight residual False 2.89 2.55 0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 1095 not shown) Planarity restraints: 1028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 307 " -0.014 2.00e-02 2.50e+03 1.90e-02 6.34e+00 pdb=" CG PHE C 307 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE C 307 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE C 307 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE C 307 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 307 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 307 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 307 " -0.014 2.00e-02 2.50e+03 1.90e-02 6.33e+00 pdb=" CG PHE A 307 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 307 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 307 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE A 307 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 307 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 307 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 319 " -0.209 9.50e-02 1.11e+02 9.39e-02 5.42e+00 pdb=" NE ARG A 319 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 319 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 319 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 319 " -0.007 2.00e-02 2.50e+03 ... (remaining 1025 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 80 2.67 - 3.23: 5929 3.23 - 3.79: 9615 3.79 - 4.34: 13121 4.34 - 4.90: 22115 Nonbonded interactions: 50860 Sorted by model distance: nonbonded pdb=" O LEU A 302 " pdb=" OG1 THR A 306 " model vdw 2.116 3.040 nonbonded pdb=" O LEU C 302 " pdb=" OG1 THR C 306 " model vdw 2.117 3.040 nonbonded pdb=" O MET C 309 " pdb=" OG1 THR C 313 " model vdw 2.199 3.040 nonbonded pdb=" O MET A 309 " pdb=" OG1 THR A 313 " model vdw 2.200 3.040 nonbonded pdb=" O VAL D 47 " pdb=" OG SER D 51 " model vdw 2.234 3.040 ... (remaining 50855 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 403 or resid 405 through 410 or resid 412 throug \ h 413)) selection = (chain 'C' and (resid 2 through 403 or resid 405 through 410 or resid 412 throug \ h 413)) } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.010 Normalize map: mean=0, sd=1: 0.800 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.630 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 : 0.005 0.109 6940 Z= 0.281 Angle : 0.827 12.227 9332 Z= 0.415 Chirality : 0.048 0.471 1098 Planarity : 0.008 0.094 1028 Dihedral : 14.925 82.617 3414 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.30), residues: 752 helix: 1.89 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -1.65 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 169 TYR 0.012 0.002 TYR A 326 PHE 0.043 0.002 PHE C 307 TRP 0.010 0.001 TRP D 26 HIS 0.005 0.002 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.28 ( 6924) covalent geometry : angle 0.82737 / 0.41 ( 9328) SS BOND : bond 0.00157 / 0.08 ( 2) SS BOND : angle 0.69810 / 0.37 ( 4) hydrogen bonds : bond 0.11749 / 7.42 ( 438) hydrogen bonds : angle 5.13305 / 3.68 ( 1314) Misc. bond : bond 0.00050 / 0.03 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.255 Fit side-chains REVERT: A 70 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7287 (tp30) REVERT: A 154 MET cc_start: 0.8309 (mtt) cc_final: 0.7988 (mtt) REVERT: A 175 LYS cc_start: 0.8302 (mmmm) cc_final: 0.7977 (mtpm) REVERT: A 178 GLN cc_start: 0.7493 (mt0) cc_final: 0.7290 (mp10) REVERT: A 220 TRP cc_start: 0.7185 (m100) cc_final: 0.6646 (m-10) REVERT: A 288 TYR cc_start: 0.7817 (m-80) cc_final: 0.7438 (m-80) REVERT: B 52 MET cc_start: 0.6977 (mmm) cc_final: 0.6655 (ttp) REVERT: B 67 MET cc_start: 0.4853 (tmm) cc_final: 0.3880 (ptt) REVERT: C 70 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7295 (tp30) REVERT: C 154 MET cc_start: 0.8300 (mtt) cc_final: 0.7914 (mtt) REVERT: C 178 GLN cc_start: 0.7442 (mt0) cc_final: 0.7213 (mp10) REVERT: C 220 TRP cc_start: 0.7312 (m100) cc_final: 0.6802 (m-10) REVERT: C 288 TYR cc_start: 0.7925 (m-80) cc_final: 0.7602 (m-80) REVERT: C 319 ARG cc_start: 0.8095 (ptm160) cc_final: 0.7859 (ptm160) REVERT: D 67 MET cc_start: 0.4856 (tmm) cc_final: 0.3914 (ptt) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.4186 time to fit residues: 66.4389 Evaluate side-chains 135 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.181689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.130704 restraints weight = 7382.764| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.91 r_work: 0.3326 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6940 Z= 0.141 Angle : 0.554 8.022 9332 Z= 0.271 Chirality : 0.037 0.138 1098 Planarity : 0.005 0.048 1028 Dihedral : 10.454 55.610 2006 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.26 % Allowed : 21.84 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.30), residues: 752 helix: 2.63 (0.21), residues: 574 sheet: None (None), residues: 0 loop : -1.60 (0.41), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 319 TYR 0.021 0.002 TYR C 123 PHE 0.009 0.001 PHE A 127 TRP 0.009 0.001 TRP A 220 HIS 0.003 0.001 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 6924) covalent geometry : angle 0.55370 / 0.27 ( 9328) SS BOND : bond 0.00263 / 0.13 ( 2) SS BOND : angle 0.76472 / 0.41 ( 4) hydrogen bonds : bond 0.05469 / 3.57 ( 438) hydrogen bonds : angle 3.73504 / 2.69 ( 1314) Misc. bond : bond 0.00034 / 0.02 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.240 Fit side-chains REVERT: A 35 GLN cc_start: 0.8488 (mm110) cc_final: 0.8130 (pt0) REVERT: A 70 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7420 (tp30) REVERT: A 154 MET cc_start: 0.8421 (mtt) cc_final: 0.8036 (mtt) REVERT: A 178 GLN cc_start: 0.7489 (mt0) cc_final: 0.7236 (mm110) REVERT: A 207 TYR cc_start: 0.8328 (t80) cc_final: 0.7871 (t80) REVERT: A 220 TRP cc_start: 0.7320 (m100) cc_final: 0.6819 (m-10) REVERT: A 288 TYR cc_start: 0.7969 (m-80) cc_final: 0.7564 (m-80) REVERT: A 319 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7443 (ttp-110) REVERT: B 52 MET cc_start: 0.7113 (mmm) cc_final: 0.6665 (mtp) REVERT: B 67 MET cc_start: 0.4686 (tmm) cc_final: 0.3728 (ptt) REVERT: C 35 GLN cc_start: 0.8531 (mm110) cc_final: 0.8177 (pt0) REVERT: C 41 GLN cc_start: 0.8724 (mt0) cc_final: 0.8395 (mp10) REVERT: C 70 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7485 (tp30) REVERT: C 134 MET cc_start: 0.8510 (mtt) cc_final: 0.8130 (mtt) REVERT: C 154 MET cc_start: 0.8366 (mtt) cc_final: 0.7996 (mtt) REVERT: C 178 GLN cc_start: 0.7467 (mt0) cc_final: 0.7200 (mm110) REVERT: C 220 TRP cc_start: 0.7365 (m100) cc_final: 0.6844 (m-10) REVERT: C 249 GLU cc_start: 0.7636 (pm20) cc_final: 0.7268 (pm20) REVERT: C 288 TYR cc_start: 0.7953 (m-80) cc_final: 0.7606 (m-80) REVERT: C 319 ARG cc_start: 0.8351 (ptm160) cc_final: 0.8018 (ptm160) REVERT: D 67 MET cc_start: 0.4484 (tmm) cc_final: 0.3451 (ptt) outliers start: 15 outliers final: 5 residues processed: 148 average time/residue: 0.4627 time to fit residues: 72.4853 Evaluate side-chains 137 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.181678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.130845 restraints weight = 7312.655| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.91 r_work: 0.3328 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6940 Z= 0.123 Angle : 0.519 7.436 9332 Z= 0.254 Chirality : 0.036 0.150 1098 Planarity : 0.005 0.045 1028 Dihedral : 10.227 59.725 2006 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.16 % Allowed : 22.29 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.30), residues: 752 helix: 2.86 (0.21), residues: 574 sheet: None (None), residues: 0 loop : -1.58 (0.41), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.017 0.001 TYR C 123 PHE 0.010 0.001 PHE C 127 TRP 0.008 0.001 TRP C 220 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 6924) covalent geometry : angle 0.51892 / 0.25 ( 9328) SS BOND : bond 0.00271 / 0.14 ( 2) SS BOND : angle 0.74051 / 0.39 ( 4) hydrogen bonds : bond 0.05026 / 3.30 ( 438) hydrogen bonds : angle 3.54825 / 2.56 ( 1314) Misc. bond : bond 0.00024 / 0.02 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.154 Fit side-chains REVERT: A 35 GLN cc_start: 0.8488 (mm110) cc_final: 0.8143 (pt0) REVERT: A 70 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7366 (tp30) REVERT: A 154 MET cc_start: 0.8417 (mtt) cc_final: 0.8049 (mtt) REVERT: A 207 TYR cc_start: 0.8348 (t80) cc_final: 0.7892 (t80) REVERT: A 220 TRP cc_start: 0.7293 (m100) cc_final: 0.6825 (m-10) REVERT: A 288 TYR cc_start: 0.7807 (m-80) cc_final: 0.7430 (m-80) REVERT: A 320 LYS cc_start: 0.8392 (ttmm) cc_final: 0.8073 (mttt) REVERT: B 52 MET cc_start: 0.7159 (mmm) cc_final: 0.6705 (mtp) REVERT: B 67 MET cc_start: 0.4518 (tmm) cc_final: 0.3580 (ptt) REVERT: C 35 GLN cc_start: 0.8504 (mm110) cc_final: 0.8162 (pt0) REVERT: C 70 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7447 (tp30) REVERT: C 154 MET cc_start: 0.8339 (mtt) cc_final: 0.7994 (mtt) REVERT: C 169 ARG cc_start: 0.7807 (mtp85) cc_final: 0.7380 (mtt180) REVERT: C 178 GLN cc_start: 0.7515 (mt0) cc_final: 0.7244 (mm110) REVERT: C 220 TRP cc_start: 0.7384 (m100) cc_final: 0.6877 (m-10) REVERT: C 288 TYR cc_start: 0.7917 (m-80) cc_final: 0.7544 (m-80) REVERT: C 319 ARG cc_start: 0.8449 (ptm160) cc_final: 0.8007 (ptm160) REVERT: D 52 MET cc_start: 0.7121 (mmm) cc_final: 0.6627 (mtp) REVERT: D 67 MET cc_start: 0.4521 (tmm) cc_final: 0.3585 (ptt) outliers start: 21 outliers final: 6 residues processed: 145 average time/residue: 0.4347 time to fit residues: 66.9437 Evaluate side-chains 133 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 GLN C 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.177553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.125974 restraints weight = 7387.028| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.89 r_work: 0.3272 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6940 Z= 0.173 Angle : 0.568 7.602 9332 Z= 0.277 Chirality : 0.038 0.159 1098 Planarity : 0.005 0.050 1028 Dihedral : 10.821 57.298 2006 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.46 % Allowed : 22.14 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.30), residues: 752 helix: 2.74 (0.21), residues: 574 sheet: None (None), residues: 0 loop : -1.61 (0.41), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.014 0.002 TYR C 123 PHE 0.012 0.002 PHE C 127 TRP 0.010 0.001 TRP A 220 HIS 0.003 0.001 HIS C 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 6924) covalent geometry : angle 0.56730 / 0.28 ( 9328) SS BOND : bond 0.00377 / 0.19 ( 2) SS BOND : angle 1.04515 / 0.55 ( 4) hydrogen bonds : bond 0.05892 / 3.89 ( 438) hydrogen bonds : angle 3.70028 / 2.66 ( 1314) Misc. bond : bond 0.00036 / 0.02 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.195 Fit side-chains REVERT: A 35 GLN cc_start: 0.8461 (mm110) cc_final: 0.8137 (pt0) REVERT: A 70 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7446 (tp30) REVERT: A 150 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.7038 (p0) REVERT: A 154 MET cc_start: 0.8492 (mtt) cc_final: 0.8138 (mtt) REVERT: A 207 TYR cc_start: 0.8443 (t80) cc_final: 0.8151 (t80) REVERT: A 220 TRP cc_start: 0.7434 (m100) cc_final: 0.6941 (m-10) REVERT: A 222 ASN cc_start: 0.7975 (m110) cc_final: 0.7713 (m-40) REVERT: A 288 TYR cc_start: 0.7928 (m-80) cc_final: 0.7624 (m-80) REVERT: A 320 LYS cc_start: 0.8512 (ttmm) cc_final: 0.8273 (mttt) REVERT: B 52 MET cc_start: 0.7175 (mmm) cc_final: 0.6700 (mtp) REVERT: B 67 MET cc_start: 0.4550 (tmm) cc_final: 0.3660 (ptt) REVERT: C 35 GLN cc_start: 0.8455 (mm110) cc_final: 0.8142 (pt0) REVERT: C 70 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7520 (tp30) REVERT: C 150 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7028 (p0) REVERT: C 154 MET cc_start: 0.8357 (mtt) cc_final: 0.8008 (mtt) REVERT: C 207 TYR cc_start: 0.8435 (t80) cc_final: 0.8155 (t80) REVERT: C 220 TRP cc_start: 0.7450 (m100) cc_final: 0.6936 (m-10) REVERT: C 222 ASN cc_start: 0.7944 (m110) cc_final: 0.7678 (m-40) REVERT: C 288 TYR cc_start: 0.8018 (m-80) cc_final: 0.7684 (m-80) REVERT: C 319 ARG cc_start: 0.8545 (ptm160) cc_final: 0.7970 (ptm160) REVERT: C 320 LYS cc_start: 0.8377 (mttt) cc_final: 0.8067 (ttmm) REVERT: D 52 MET cc_start: 0.7138 (mmm) cc_final: 0.6625 (mtp) REVERT: D 67 MET cc_start: 0.4318 (tmm) cc_final: 0.3528 (ptt) outliers start: 23 outliers final: 7 residues processed: 146 average time/residue: 0.4501 time to fit residues: 69.5293 Evaluate side-chains 131 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 4 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 71 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 0.0670 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 GLN A 260 GLN C 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.181524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.130415 restraints weight = 7362.646| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.90 r_work: 0.3330 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6940 Z= 0.114 Angle : 0.516 9.063 9332 Z= 0.250 Chirality : 0.036 0.152 1098 Planarity : 0.005 0.044 1028 Dihedral : 10.147 59.503 2006 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.86 % Allowed : 23.64 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.30), residues: 752 helix: 2.94 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -1.50 (0.42), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.013 0.001 TYR C 123 PHE 0.009 0.001 PHE A 127 TRP 0.007 0.001 TRP B 26 HIS 0.003 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 6924) covalent geometry : angle 0.51564 / 0.25 ( 9328) SS BOND : bond 0.00245 / 0.12 ( 2) SS BOND : angle 0.60266 / 0.32 ( 4) hydrogen bonds : bond 0.04768 / 3.13 ( 438) hydrogen bonds : angle 3.47687 / 2.51 ( 1314) Misc. bond : bond 0.00014 / 0.01 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8487 (mm110) cc_final: 0.8164 (pt0) REVERT: A 41 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8230 (mp10) REVERT: A 50 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: A 70 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7345 (tp30) REVERT: A 150 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.6985 (p0) REVERT: A 207 TYR cc_start: 0.8383 (t80) cc_final: 0.7979 (t80) REVERT: A 220 TRP cc_start: 0.7298 (m100) cc_final: 0.6852 (m-10) REVERT: A 288 TYR cc_start: 0.7865 (m-80) cc_final: 0.7481 (m-80) REVERT: B 52 MET cc_start: 0.7115 (mmm) cc_final: 0.6608 (mtp) REVERT: B 67 MET cc_start: 0.4610 (tmm) cc_final: 0.3769 (ptt) REVERT: C 35 GLN cc_start: 0.8486 (mm110) cc_final: 0.8177 (pt0) REVERT: C 50 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: C 70 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7391 (tp30) REVERT: C 154 MET cc_start: 0.8307 (mtt) cc_final: 0.7958 (mtt) REVERT: C 169 ARG cc_start: 0.7791 (mtp85) cc_final: 0.7072 (mtt180) REVERT: C 178 GLN cc_start: 0.7373 (mt0) cc_final: 0.7139 (mp10) REVERT: C 207 TYR cc_start: 0.8413 (t80) cc_final: 0.8006 (t80) REVERT: C 220 TRP cc_start: 0.7363 (m100) cc_final: 0.6864 (m-10) REVERT: C 288 TYR cc_start: 0.7874 (m-80) cc_final: 0.7519 (m-80) REVERT: C 319 ARG cc_start: 0.8529 (ptm160) cc_final: 0.7995 (ptm160) REVERT: C 320 LYS cc_start: 0.8251 (mttt) cc_final: 0.7949 (ttmm) REVERT: D 52 MET cc_start: 0.7066 (mmm) cc_final: 0.6598 (mtp) REVERT: D 67 MET cc_start: 0.4406 (tmm) cc_final: 0.3664 (ptt) outliers start: 19 outliers final: 6 residues processed: 144 average time/residue: 0.4836 time to fit residues: 73.5821 Evaluate side-chains 139 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 3 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 41 GLN C 156 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.176605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.124337 restraints weight = 7460.891| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.93 r_work: 0.3265 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6940 Z= 0.182 Angle : 0.594 8.366 9332 Z= 0.288 Chirality : 0.039 0.159 1098 Planarity : 0.005 0.049 1028 Dihedral : 10.721 53.595 2006 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.77 % Allowed : 22.59 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.30), residues: 752 helix: 2.75 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -1.58 (0.42), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.015 0.002 TYR C 207 PHE 0.013 0.002 PHE A 127 TRP 0.010 0.001 TRP A 220 HIS 0.004 0.001 HIS A 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 ( 6924) covalent geometry : angle 0.59329 / 0.29 ( 9328) SS BOND : bond 0.00408 / 0.20 ( 2) SS BOND : angle 1.09015 / 0.58 ( 4) hydrogen bonds : bond 0.05871 / 3.89 ( 438) hydrogen bonds : angle 3.68657 / 2.65 ( 1314) Misc. bond : bond 0.00033 / 0.02 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.237 Fit side-chains REVERT: A 35 GLN cc_start: 0.8477 (mm110) cc_final: 0.8154 (pt0) REVERT: A 50 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: A 70 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7465 (tp30) REVERT: A 150 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7031 (p0) REVERT: A 154 MET cc_start: 0.8441 (mtt) cc_final: 0.8048 (mtt) REVERT: A 178 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7559 (mt0) REVERT: A 207 TYR cc_start: 0.8590 (t80) cc_final: 0.8311 (t80) REVERT: A 220 TRP cc_start: 0.7434 (m100) cc_final: 0.6941 (m-10) REVERT: A 222 ASN cc_start: 0.7888 (m110) cc_final: 0.7662 (m-40) REVERT: A 288 TYR cc_start: 0.7952 (m-80) cc_final: 0.7618 (m-80) REVERT: B 52 MET cc_start: 0.7117 (mmm) cc_final: 0.6602 (mtp) REVERT: B 55 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6746 (tt) REVERT: B 67 MET cc_start: 0.4398 (tmm) cc_final: 0.3662 (ptt) REVERT: C 35 GLN cc_start: 0.8483 (mm110) cc_final: 0.8169 (pt0) REVERT: C 41 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8325 (mp10) REVERT: C 50 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: C 70 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7489 (tp30) REVERT: C 150 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.6926 (p0) REVERT: C 154 MET cc_start: 0.8305 (mtt) cc_final: 0.7966 (mtt) REVERT: C 179 LEU cc_start: 0.7953 (tp) cc_final: 0.7686 (mm) REVERT: C 207 TYR cc_start: 0.8579 (t80) cc_final: 0.8304 (t80) REVERT: C 220 TRP cc_start: 0.7450 (m100) cc_final: 0.6945 (m-10) REVERT: C 222 ASN cc_start: 0.7873 (m110) cc_final: 0.7647 (m-40) REVERT: C 288 TYR cc_start: 0.7972 (m-80) cc_final: 0.7611 (m-80) REVERT: C 319 ARG cc_start: 0.8575 (ptm160) cc_final: 0.8040 (ptm160) REVERT: D 52 MET cc_start: 0.7112 (mmm) cc_final: 0.6624 (mtp) REVERT: D 67 MET cc_start: 0.4376 (tmm) cc_final: 0.3653 (ptt) outliers start: 25 outliers final: 12 residues processed: 139 average time/residue: 0.4385 time to fit residues: 64.6809 Evaluate side-chains 138 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.0370 chunk 10 optimal weight: 0.0670 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 GLN C 260 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.181346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.130241 restraints weight = 7322.164| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.91 r_work: 0.3331 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6940 Z= 0.115 Angle : 0.527 8.245 9332 Z= 0.256 Chirality : 0.036 0.170 1098 Planarity : 0.005 0.044 1028 Dihedral : 9.995 53.690 2006 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.86 % Allowed : 23.95 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.30), residues: 752 helix: 2.96 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -1.52 (0.42), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.012 0.001 TYR C 123 PHE 0.010 0.001 PHE C 256 TRP 0.008 0.001 TRP B 26 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 ( 6924) covalent geometry : angle 0.52653 / 0.26 ( 9328) SS BOND : bond 0.00250 / 0.13 ( 2) SS BOND : angle 0.58334 / 0.31 ( 4) hydrogen bonds : bond 0.04692 / 3.09 ( 438) hydrogen bonds : angle 3.48559 / 2.52 ( 1314) Misc. bond : bond 0.00013 / 0.01 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.242 Fit side-chains REVERT: A 35 GLN cc_start: 0.8517 (mm110) cc_final: 0.8171 (pt0) REVERT: A 50 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6728 (mp0) REVERT: A 70 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7328 (tp30) REVERT: A 154 MET cc_start: 0.8473 (mtt) cc_final: 0.8067 (mtt) REVERT: A 207 TYR cc_start: 0.8643 (t80) cc_final: 0.8325 (t80) REVERT: A 220 TRP cc_start: 0.7319 (m100) cc_final: 0.6834 (m-10) REVERT: A 288 TYR cc_start: 0.7881 (m-80) cc_final: 0.7530 (m-80) REVERT: A 320 LYS cc_start: 0.8384 (ttmm) cc_final: 0.8106 (mttt) REVERT: B 52 MET cc_start: 0.7261 (mmm) cc_final: 0.6727 (mtp) REVERT: B 67 MET cc_start: 0.4453 (tmm) cc_final: 0.3771 (ptt) REVERT: C 35 GLN cc_start: 0.8549 (mm110) cc_final: 0.8213 (pt0) REVERT: C 50 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: C 70 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7359 (tp30) REVERT: C 150 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6902 (p0) REVERT: C 154 MET cc_start: 0.8262 (mtt) cc_final: 0.8032 (mtt) REVERT: C 169 ARG cc_start: 0.7823 (mtp85) cc_final: 0.7208 (mtt180) REVERT: C 178 GLN cc_start: 0.7558 (mt0) cc_final: 0.7322 (mp10) REVERT: C 207 TYR cc_start: 0.8627 (t80) cc_final: 0.8296 (t80) REVERT: C 220 TRP cc_start: 0.7413 (m100) cc_final: 0.6944 (m-10) REVERT: C 288 TYR cc_start: 0.7917 (m-80) cc_final: 0.7591 (m-80) REVERT: C 319 ARG cc_start: 0.8556 (ptm160) cc_final: 0.7937 (ptm160) REVERT: C 320 LYS cc_start: 0.8212 (mttt) cc_final: 0.7941 (ttmm) REVERT: D 52 MET cc_start: 0.7129 (mmm) cc_final: 0.6625 (mtp) REVERT: D 67 MET cc_start: 0.4297 (tmm) cc_final: 0.3684 (ptt) outliers start: 19 outliers final: 5 residues processed: 145 average time/residue: 0.4791 time to fit residues: 73.4974 Evaluate side-chains 133 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 5 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 0.0770 chunk 1 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 GLN A 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.181751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.130968 restraints weight = 7454.421| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.91 r_work: 0.3331 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6940 Z= 0.119 Angle : 0.538 8.656 9332 Z= 0.263 Chirality : 0.036 0.188 1098 Planarity : 0.005 0.044 1028 Dihedral : 9.703 54.009 2006 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.41 % Allowed : 24.10 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.06 (0.30), residues: 752 helix: 2.98 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -1.47 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.012 0.001 TYR C 123 PHE 0.011 0.001 PHE C 127 TRP 0.007 0.001 TRP B 26 HIS 0.002 0.000 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 6924) covalent geometry : angle 0.53757 / 0.26 ( 9328) SS BOND : bond 0.00252 / 0.13 ( 2) SS BOND : angle 0.58396 / 0.31 ( 4) hydrogen bonds : bond 0.04619 / 3.04 ( 438) hydrogen bonds : angle 3.47781 / 2.52 ( 1314) Misc. bond : bond 0.00015 / 0.01 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.244 Fit side-chains REVERT: A 35 GLN cc_start: 0.8517 (mm110) cc_final: 0.8174 (pt0) REVERT: A 50 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6703 (mp0) REVERT: A 70 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7340 (tp30) REVERT: A 150 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.6962 (p0) REVERT: A 154 MET cc_start: 0.8306 (mtt) cc_final: 0.8023 (mtt) REVERT: A 178 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7451 (mp10) REVERT: A 207 TYR cc_start: 0.8645 (t80) cc_final: 0.8329 (t80) REVERT: A 220 TRP cc_start: 0.7315 (m100) cc_final: 0.6870 (m-10) REVERT: A 288 TYR cc_start: 0.7854 (m-80) cc_final: 0.7455 (m-80) REVERT: B 52 MET cc_start: 0.7280 (mmm) cc_final: 0.6729 (mtp) REVERT: B 55 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6680 (tt) REVERT: B 67 MET cc_start: 0.4429 (tmm) cc_final: 0.3774 (ptt) REVERT: C 35 GLN cc_start: 0.8552 (mm110) cc_final: 0.8199 (pt0) REVERT: C 50 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: C 70 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7365 (tp30) REVERT: C 150 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.6893 (p0) REVERT: C 154 MET cc_start: 0.8314 (mtt) cc_final: 0.8060 (mtt) REVERT: C 169 ARG cc_start: 0.7836 (mtp85) cc_final: 0.7218 (mtt180) REVERT: C 178 GLN cc_start: 0.7531 (mt0) cc_final: 0.7311 (mp10) REVERT: C 207 TYR cc_start: 0.8598 (t80) cc_final: 0.8249 (t80) REVERT: C 220 TRP cc_start: 0.7407 (m100) cc_final: 0.6941 (m-10) REVERT: C 288 TYR cc_start: 0.7886 (m-80) cc_final: 0.7510 (m-80) REVERT: C 319 ARG cc_start: 0.8559 (ptm160) cc_final: 0.7944 (ptm160) REVERT: D 52 MET cc_start: 0.7276 (mmm) cc_final: 0.6754 (mtp) REVERT: D 67 MET cc_start: 0.4306 (tmm) cc_final: 0.3702 (ptt) outliers start: 16 outliers final: 8 residues processed: 139 average time/residue: 0.4629 time to fit residues: 68.0816 Evaluate side-chains 134 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 25 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.181761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.130765 restraints weight = 7402.499| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.90 r_work: 0.3338 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6940 Z= 0.121 Angle : 0.544 8.569 9332 Z= 0.267 Chirality : 0.037 0.194 1098 Planarity : 0.005 0.043 1028 Dihedral : 9.535 54.342 2006 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.96 % Allowed : 25.30 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.06 (0.31), residues: 752 helix: 2.96 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -1.40 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.012 0.001 TYR C 123 PHE 0.010 0.001 PHE A 127 TRP 0.007 0.001 TRP B 26 HIS 0.002 0.000 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 6924) covalent geometry : angle 0.54398 / 0.27 ( 9328) SS BOND : bond 0.00258 / 0.13 ( 2) SS BOND : angle 0.60517 / 0.32 ( 4) hydrogen bonds : bond 0.04642 / 3.06 ( 438) hydrogen bonds : angle 3.49081 / 2.53 ( 1314) Misc. bond : bond 0.00015 / 0.01 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.167 Fit side-chains REVERT: A 35 GLN cc_start: 0.8529 (mm110) cc_final: 0.8188 (pt0) REVERT: A 50 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6645 (mp0) REVERT: A 70 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7351 (tp30) REVERT: A 150 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.6952 (p0) REVERT: A 154 MET cc_start: 0.8286 (mtt) cc_final: 0.7906 (mtt) REVERT: A 169 ARG cc_start: 0.7565 (mtt-85) cc_final: 0.7152 (mtt180) REVERT: A 207 TYR cc_start: 0.8605 (t80) cc_final: 0.8271 (t80) REVERT: A 220 TRP cc_start: 0.7370 (m100) cc_final: 0.6925 (m-10) REVERT: A 288 TYR cc_start: 0.7867 (m-80) cc_final: 0.7520 (m-80) REVERT: B 52 MET cc_start: 0.7316 (mmm) cc_final: 0.6752 (mtp) REVERT: B 55 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6666 (tt) REVERT: B 67 MET cc_start: 0.4405 (tmm) cc_final: 0.3784 (ptt) REVERT: C 35 GLN cc_start: 0.8555 (mm110) cc_final: 0.8213 (pt0) REVERT: C 50 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6714 (mp0) REVERT: C 70 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7370 (tp30) REVERT: C 150 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.6956 (p0) REVERT: C 154 MET cc_start: 0.8310 (mtt) cc_final: 0.8015 (mtt) REVERT: C 169 ARG cc_start: 0.7830 (mtp85) cc_final: 0.7306 (mtt180) REVERT: C 178 GLN cc_start: 0.7476 (mt0) cc_final: 0.7262 (mp10) REVERT: C 207 TYR cc_start: 0.8601 (t80) cc_final: 0.8257 (t80) REVERT: C 220 TRP cc_start: 0.7418 (m100) cc_final: 0.6954 (m-10) REVERT: C 288 TYR cc_start: 0.7897 (m-80) cc_final: 0.7514 (m-80) REVERT: C 319 ARG cc_start: 0.8566 (ptm160) cc_final: 0.7971 (ptm160) REVERT: D 52 MET cc_start: 0.7319 (mmm) cc_final: 0.6780 (mtp) REVERT: D 67 MET cc_start: 0.4295 (tmm) cc_final: 0.3648 (ptt) outliers start: 13 outliers final: 8 residues processed: 135 average time/residue: 0.4536 time to fit residues: 64.7391 Evaluate side-chains 136 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 19 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 68 optimal weight: 0.2980 chunk 37 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.177434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.125613 restraints weight = 7423.210| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.91 r_work: 0.3275 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 6940 Z= 0.163 Angle : 0.603 9.498 9332 Z= 0.298 Chirality : 0.039 0.230 1098 Planarity : 0.005 0.048 1028 Dihedral : 10.202 59.445 2006 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.26 % Allowed : 25.30 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.30), residues: 752 helix: 2.78 (0.20), residues: 576 sheet: None (None), residues: 0 loop : -1.52 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 241 TYR 0.015 0.002 TYR C 123 PHE 0.013 0.002 PHE A 127 TRP 0.009 0.001 TRP A 220 HIS 0.003 0.001 HIS C 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 6924) covalent geometry : angle 0.60300 / 0.30 ( 9328) SS BOND : bond 0.00360 / 0.18 ( 2) SS BOND : angle 1.05066 / 0.55 ( 4) hydrogen bonds : bond 0.05601 / 3.72 ( 438) hydrogen bonds : angle 3.68416 / 2.67 ( 1314) Misc. bond : bond 0.00025 / 0.02 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.195 Fit side-chains REVERT: A 35 GLN cc_start: 0.8525 (mm110) cc_final: 0.8189 (pt0) REVERT: A 50 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: A 70 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7451 (tp30) REVERT: A 150 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.6967 (p0) REVERT: A 154 MET cc_start: 0.8371 (mtt) cc_final: 0.8011 (mtt) REVERT: A 169 ARG cc_start: 0.7564 (mtt-85) cc_final: 0.7228 (mtt180) REVERT: A 220 TRP cc_start: 0.7477 (m100) cc_final: 0.7006 (m-10) REVERT: A 222 ASN cc_start: 0.7845 (m110) cc_final: 0.7620 (m-40) REVERT: A 288 TYR cc_start: 0.7931 (m-80) cc_final: 0.7588 (m-80) REVERT: A 320 LYS cc_start: 0.8543 (ttmm) cc_final: 0.8290 (mttt) REVERT: B 52 MET cc_start: 0.7019 (mmm) cc_final: 0.6428 (mtp) REVERT: B 67 MET cc_start: 0.4565 (tmm) cc_final: 0.3966 (ptt) REVERT: C 35 GLN cc_start: 0.8546 (mm110) cc_final: 0.8184 (pt0) REVERT: C 50 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: C 70 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7491 (tp30) REVERT: C 150 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.6920 (p0) REVERT: C 154 MET cc_start: 0.8357 (mtt) cc_final: 0.8137 (mtt) REVERT: C 169 ARG cc_start: 0.7703 (mtp85) cc_final: 0.7466 (mtp85) REVERT: C 178 GLN cc_start: 0.7573 (mt0) cc_final: 0.7357 (mp10) REVERT: C 220 TRP cc_start: 0.7529 (m100) cc_final: 0.7039 (m-10) REVERT: C 222 ASN cc_start: 0.7847 (m110) cc_final: 0.7624 (m-40) REVERT: C 249 GLU cc_start: 0.7772 (pm20) cc_final: 0.7563 (pm20) REVERT: C 288 TYR cc_start: 0.7946 (m-80) cc_final: 0.7602 (m-80) REVERT: C 319 ARG cc_start: 0.8564 (ptm160) cc_final: 0.8112 (ptm160) REVERT: D 52 MET cc_start: 0.7334 (mmm) cc_final: 0.6792 (mtp) REVERT: D 67 MET cc_start: 0.4332 (tmm) cc_final: 0.3662 (ptt) outliers start: 15 outliers final: 7 residues processed: 131 average time/residue: 0.4930 time to fit residues: 68.1843 Evaluate side-chains 131 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 0.0170 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 20 optimal weight: 0.0000 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.181527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.130620 restraints weight = 7379.035| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.90 r_work: 0.3331 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6940 Z= 0.121 Angle : 0.559 10.390 9332 Z= 0.276 Chirality : 0.037 0.235 1098 Planarity : 0.005 0.043 1028 Dihedral : 9.594 55.525 2006 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.11 % Allowed : 25.45 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.10 (0.30), residues: 752 helix: 3.03 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -1.42 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 44 TYR 0.012 0.001 TYR C 123 PHE 0.013 0.001 PHE A 256 TRP 0.008 0.001 TRP B 26 HIS 0.002 0.000 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 6924) covalent geometry : angle 0.55948 / 0.28 ( 9328) SS BOND : bond 0.00261 / 0.13 ( 2) SS BOND : angle 0.53126 / 0.28 ( 4) hydrogen bonds : bond 0.04635 / 3.06 ( 438) hydrogen bonds : angle 3.51748 / 2.55 ( 1314) Misc. bond : bond 0.00013 / 0.01 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2532.77 seconds wall clock time: 43 minutes 50.43 seconds (2630.43 seconds total)