Starting phenix.real_space_refine on Thu Jul 2 05:58:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wqr_66180/07_2026/9wqr_66180.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wqr_66180/07_2026/9wqr_66180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wqr_66180/07_2026/9wqr_66180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wqr_66180/07_2026/9wqr_66180.map" model { file = "/net/cci-nas-00/data/ceres_data/9wqr_66180/07_2026/9wqr_66180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wqr_66180/07_2026/9wqr_66180.cif" } resolution = 2.79 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= 0.003 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 54 5.16 5 Cl 4 4.86 5 C 4750 2.51 5 N 978 2.21 5 O 1138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s 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: 6930 Number of models: 1 Model: "" Number of chains: 5 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: "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: "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: "A" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 543 Unusual residues: {'CLR': 6, 'FI8': 1, 'PLM': 7, 'POV': 4} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PLM:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 451 Unusual residues: {'CLR': 6, 'FI8': 1, 'PLM': 7, 'POV': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PLM:plan-1': 7} Unresolved non-hydrogen planarities: 7 Restraints were copied for chains: D Time building chain proxies: 1.97, per 1000 atoms: 0.28 Number of scatterers: 6930 At special positions: 0 Unit cell: (86.9, 89.1, 93.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 54 16.00 P 6 15.00 O 1138 8.00 N 978 7.00 C 4750 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=2.04 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: 0.56 Conformation dependent library (CDL) restraints added in 356.8 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: 28 helices and 0 sheets defined 77.9% 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 'B' and resid 17 through 28 Processing helix chain 'B' and resid 33 through 68 Processing helix chain 'A' and resid 15 through 27 removed outlier: 3.707A pdb=" N VAL A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 27 " --> pdb=" O LYS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 34 removed outlier: 3.806A pdb=" N CYS A 32 " --> pdb=" O PRO A 29 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 34 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 47 through 78 Processing helix chain 'A' and resid 81 through 93 removed outlier: 3.592A pdb=" N THR A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 108 Processing helix chain 'A' and resid 111 through 139 removed outlier: 3.850A pdb=" N SER A 121 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 3.667A 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 removed outlier: 4.157A pdb=" N GLY A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Proline residue: A 184 - end of helix Processing helix chain 'A' and resid 216 through 247 removed outlier: 3.843A pdb=" N TRP A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 279 removed outlier: 4.307A 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: 3.589A pdb=" N ARG A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 27 removed outlier: 3.707A pdb=" N VAL C 21 " --> pdb=" O ASP C 17 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 27 " --> pdb=" O LYS C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.805A pdb=" N CYS C 32 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER C 34 " --> pdb=" O ALA C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 47 through 78 Processing helix chain 'C' and resid 81 through 93 removed outlier: 3.592A pdb=" N THR C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 108 Processing helix chain 'C' and resid 111 through 139 removed outlier: 3.850A pdb=" N SER C 121 " --> pdb=" O MET C 117 " (cutoff:3.500A) removed outlier: 3.667A 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 removed outlier: 4.156A pdb=" N GLY C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 216 through 247 removed outlier: 3.843A pdb=" N TRP C 220 " --> pdb=" O SER C 216 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 279 removed outlier: 4.307A 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: 3.589A 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 68 442 hydrogen bonds defined for protein. 1320 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: 0.99 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 982 1.32 - 1.45: 1632 1.45 - 1.57: 4370 1.57 - 1.69: 12 1.69 - 1.82: 84 Bond restraints: 7080 Sorted by residual: bond pdb=" N VAL B 30 " pdb=" CA VAL B 30 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.17e-02 7.31e+03 7.32e+00 bond pdb=" N VAL D 30 " pdb=" CA VAL D 30 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.17e-02 7.31e+03 7.21e+00 bond pdb=" N THR C 266 " pdb=" CA THR C 266 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.30e-02 5.92e+03 4.05e+00 bond pdb=" N THR A 266 " pdb=" CA THR A 266 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.30e-02 5.92e+03 4.01e+00 bond pdb=" C PRO A 286 " pdb=" N PRO A 287 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.94e+00 ... (remaining 7075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 9085 1.49 - 2.98: 384 2.98 - 4.47: 50 4.47 - 5.96: 13 5.96 - 7.45: 18 Bond angle restraints: 9550 Sorted by residual: angle pdb=" C GLY C 248 " pdb=" N GLU C 249 " pdb=" CA GLU C 249 " ideal model delta sigma weight residual 121.54 128.43 -6.89 1.91e+00 2.74e-01 1.30e+01 angle pdb=" C GLY A 248 " pdb=" N GLU A 249 " pdb=" CA GLU A 249 " ideal model delta sigma weight residual 121.54 128.40 -6.86 1.91e+00 2.74e-01 1.29e+01 angle pdb=" CG ARG A 146 " pdb=" CD ARG A 146 " pdb=" NE ARG A 146 " ideal model delta sigma weight residual 112.00 119.32 -7.32 2.20e+00 2.07e-01 1.11e+01 angle pdb=" CG ARG C 146 " pdb=" CD ARG C 146 " pdb=" NE ARG C 146 " ideal model delta sigma weight residual 112.00 119.31 -7.31 2.20e+00 2.07e-01 1.10e+01 angle pdb=" CB ARG A 174 " pdb=" CG ARG A 174 " pdb=" CD ARG A 174 " ideal model delta sigma weight residual 111.30 118.75 -7.45 2.30e+00 1.89e-01 1.05e+01 ... (remaining 9545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.02: 4662 26.02 - 52.03: 318 52.03 - 78.05: 46 78.05 - 104.06: 10 104.06 - 130.08: 12 Dihedral angle restraints: 5048 sinusoidal: 2832 harmonic: 2216 Sorted by residual: dihedral pdb=" C48 FI8 C 416 " pdb=" C45 FI8 C 416 " pdb=" C46 FI8 C 416 " pdb=" O17 FI8 C 416 " ideal model delta sinusoidal sigma weight residual 49.43 -80.65 130.08 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C48 FI8 A 415 " pdb=" C45 FI8 A 415 " pdb=" C46 FI8 A 415 " pdb=" O17 FI8 A 415 " ideal model delta sinusoidal sigma weight residual 49.43 -80.63 130.06 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C44 FI8 C 416 " pdb=" C45 FI8 C 416 " pdb=" C46 FI8 C 416 " pdb=" C48 FI8 C 416 " ideal model delta sinusoidal sigma weight residual 70.00 -161.06 -128.94 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 5045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 838 0.034 - 0.069: 205 0.069 - 0.103: 64 0.103 - 0.138: 19 0.138 - 0.172: 4 Chirality restraints: 1130 Sorted by residual: chirality pdb=" CA VAL D 30 " pdb=" N VAL D 30 " pdb=" C VAL D 30 " pdb=" CB VAL D 30 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" CA VAL B 30 " pdb=" N VAL B 30 " pdb=" C VAL B 30 " pdb=" CB VAL B 30 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CB VAL D 30 " pdb=" CA VAL D 30 " pdb=" CG1 VAL D 30 " pdb=" CG2 VAL D 30 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1127 not shown) Planarity restraints: 1042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 174 " 0.182 9.50e-02 1.11e+02 8.24e-02 5.24e+00 pdb=" NE ARG C 174 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C 174 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG C 174 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 174 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 174 " -0.182 9.50e-02 1.11e+02 8.23e-02 5.24e+00 pdb=" NE ARG A 174 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 174 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG A 174 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 174 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 249 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C GLU C 249 " -0.037 2.00e-02 2.50e+03 pdb=" O GLU C 249 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN C 250 " 0.012 2.00e-02 2.50e+03 ... (remaining 1039 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 2199 2.88 - 3.39: 6534 3.39 - 3.89: 10606 3.89 - 4.40: 11749 4.40 - 4.90: 21018 Nonbonded interactions: 52106 Sorted by model distance: nonbonded pdb=" O GLU A 20 " pdb=" OG1 THR A 24 " model vdw 2.379 3.040 nonbonded pdb=" O GLU C 20 " pdb=" OG1 THR C 24 " model vdw 2.379 3.040 nonbonded pdb=" O ALA A 61 " pdb=" OG SER A 64 " model vdw 2.384 3.040 nonbonded pdb=" O ALA C 61 " pdb=" OG SER C 64 " model vdw 2.385 3.040 nonbonded pdb=" O LEU A 225 " pdb=" OG1 THR A 229 " model vdw 2.404 3.040 ... (remaining 52101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 401 or resid 403 through 404 or resid 407 throug \ h 411)) selection = (chain 'C' and (resid 2 through 401 or resid 403 through 404 or resid 407 throug \ h 411)) } 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: 0.000 Normalize map: mean=0, sd=1: 0.620 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.820 Find NCS groups from input model: 0.070 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:10.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 0.040 7096 Z= 0.238 Angle : 0.728 7.448 9554 Z= 0.378 Chirality : 0.037 0.172 1130 Planarity : 0.007 0.082 1042 Dihedral : 17.045 130.077 3606 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.00 % Allowed : 18.07 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.29), residues: 752 helix: 2.02 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.47 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 174 TYR 0.012 0.002 TYR C 326 PHE 0.013 0.001 PHE A 68 TRP 0.010 0.001 TRP D 36 HIS 0.006 0.001 HIS C 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.24 ( 7080) covalent geometry : angle 0.72798 / 0.38 ( 9550) SS BOND : bond 0.00402 / 0.20 ( 2) SS BOND : angle 0.57319 / 0.28 ( 4) hydrogen bonds : bond 0.13053 / 8.50 ( 442) hydrogen bonds : angle 4.79744 / 3.44 ( 1320) Misc. bond : bond 0.00108 / 0.07 ( 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 123 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7626 (tptp) cc_final: 0.7014 (pttt) REVERT: A 44 ARG cc_start: 0.7273 (mtm110) cc_final: 0.7007 (mtm110) REVERT: A 154 MET cc_start: 0.8036 (mmt) cc_final: 0.7715 (mmm) REVERT: A 175 LYS cc_start: 0.7951 (pttm) cc_final: 0.7117 (pttt) REVERT: C 9 LYS cc_start: 0.7758 (tptp) cc_final: 0.7051 (pttt) REVERT: C 44 ARG cc_start: 0.7186 (mtm110) cc_final: 0.6897 (mtm110) REVERT: C 154 MET cc_start: 0.8006 (mmt) cc_final: 0.7754 (mmm) REVERT: C 174 ARG cc_start: 0.7630 (mtp-110) cc_final: 0.7377 (mtp85) REVERT: C 175 LYS cc_start: 0.7966 (pttm) cc_final: 0.7099 (pttt) REVERT: D 57 ARG cc_start: 0.7174 (ttp80) cc_final: 0.6748 (ttp80) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.5421 time to fit residues: 69.9574 Evaluate side-chains 111 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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: 0.6980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.190443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.143647 restraints weight = 7453.495| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.59 r_work: 0.3487 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7096 Z= 0.124 Angle : 0.514 5.317 9554 Z= 0.257 Chirality : 0.035 0.125 1130 Planarity : 0.005 0.038 1042 Dihedral : 14.975 127.568 2198 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.41 % Allowed : 17.02 % Favored : 80.57 % 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: 3.16 (0.29), residues: 752 helix: 2.79 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -0.33 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 174 TYR 0.012 0.002 TYR A 123 PHE 0.013 0.001 PHE C 127 TRP 0.009 0.001 TRP B 26 HIS 0.004 0.001 HIS C 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 7080) covalent geometry : angle 0.51427 / 0.26 ( 9550) SS BOND : bond 0.00397 / 0.20 ( 2) SS BOND : angle 0.87076 / 0.43 ( 4) hydrogen bonds : bond 0.05607 / 3.94 ( 442) hydrogen bonds : angle 3.46410 / 2.52 ( 1320) Misc. bond : bond 0.00031 / 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 134 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7263 (mtm110) cc_final: 0.6987 (mtm110) REVERT: A 154 MET cc_start: 0.8078 (mmt) cc_final: 0.7782 (mmm) REVERT: A 175 LYS cc_start: 0.7750 (pttm) cc_final: 0.6836 (pttt) REVERT: A 241 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7630 (ttm170) REVERT: C 44 ARG cc_start: 0.7105 (mtm110) cc_final: 0.6806 (mtm110) REVERT: C 154 MET cc_start: 0.8095 (mmt) cc_final: 0.7800 (mmm) REVERT: C 174 ARG cc_start: 0.7753 (mtp-110) cc_final: 0.7542 (mtp85) REVERT: C 175 LYS cc_start: 0.7685 (pttm) cc_final: 0.6789 (pttt) REVERT: C 241 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7670 (ttm170) REVERT: D 25 LEU cc_start: 0.8022 (mt) cc_final: 0.7822 (mm) REVERT: D 57 ARG cc_start: 0.6981 (ttp80) cc_final: 0.6523 (ttp80) outliers start: 16 outliers final: 3 residues processed: 129 average time/residue: 0.5235 time to fit residues: 71.0037 Evaluate side-chains 119 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 241 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 19 optimal weight: 0.0030 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN C 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.191007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144601 restraints weight = 7345.904| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.57 r_work: 0.3498 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7096 Z= 0.115 Angle : 0.492 5.237 9554 Z= 0.243 Chirality : 0.034 0.124 1130 Planarity : 0.004 0.036 1042 Dihedral : 14.616 126.587 2198 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.01 % Allowed : 16.57 % Favored : 80.42 % 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: 3.52 (0.29), residues: 752 helix: 3.05 (0.20), residues: 576 sheet: None (None), residues: 0 loop : -0.24 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 174 TYR 0.013 0.001 TYR A 123 PHE 0.013 0.001 PHE A 127 TRP 0.009 0.001 TRP B 26 HIS 0.003 0.001 HIS A 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 ( 7080) covalent geometry : angle 0.49231 / 0.24 ( 9550) SS BOND : bond 0.00360 / 0.18 ( 2) SS BOND : angle 0.68709 / 0.34 ( 4) hydrogen bonds : bond 0.05175 / 3.66 ( 442) hydrogen bonds : angle 3.30069 / 2.39 ( 1320) Misc. bond : bond 0.00019 / 0.01 ( 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 138 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7377 (mtm110) cc_final: 0.7075 (mtm110) REVERT: A 154 MET cc_start: 0.8038 (mmt) cc_final: 0.7319 (mmm) REVERT: A 174 ARG cc_start: 0.7652 (mtp-110) cc_final: 0.7440 (mtp85) REVERT: A 175 LYS cc_start: 0.7578 (pttm) cc_final: 0.6552 (pttt) REVERT: A 241 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7640 (ttm170) REVERT: C 154 MET cc_start: 0.8054 (mmt) cc_final: 0.7277 (mmm) REVERT: C 175 LYS cc_start: 0.7596 (pttm) cc_final: 0.6658 (pttt) REVERT: C 241 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7705 (ttm170) REVERT: D 25 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7618 (mm) REVERT: D 57 ARG cc_start: 0.6999 (ttp80) cc_final: 0.6531 (ttp80) outliers start: 20 outliers final: 8 residues processed: 131 average time/residue: 0.5602 time to fit residues: 77.1059 Evaluate side-chains 121 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 241 ARG Chi-restraints excluded: chain D residue 25 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.1980 chunk 56 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN C 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.188326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.136244 restraints weight = 6991.388| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.73 r_work: 0.3369 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7096 Z= 0.132 Angle : 0.522 5.346 9554 Z= 0.256 Chirality : 0.035 0.127 1130 Planarity : 0.004 0.038 1042 Dihedral : 14.560 125.933 2198 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.56 % Allowed : 17.32 % Favored : 80.12 % 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: 3.43 (0.29), residues: 752 helix: 3.04 (0.20), residues: 570 sheet: None (None), residues: 0 loop : -0.36 (0.44), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 319 TYR 0.014 0.001 TYR A 123 PHE 0.015 0.001 PHE C 127 TRP 0.010 0.001 TRP C 220 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 7080) covalent geometry : angle 0.52159 / 0.26 ( 9550) SS BOND : bond 0.00644 / 0.32 ( 2) SS BOND : angle 0.62283 / 0.32 ( 4) hydrogen bonds : bond 0.05691 / 4.03 ( 442) hydrogen bonds : angle 3.38351 / 2.45 ( 1320) Misc. bond : bond 0.00024 / 0.01 ( 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 129 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ILE cc_start: 0.8597 (mm) cc_final: 0.8131 (tp) REVERT: A 44 ARG cc_start: 0.6976 (mtm110) cc_final: 0.6689 (mtm110) REVERT: A 174 ARG cc_start: 0.7460 (mtp-110) cc_final: 0.7243 (mtp85) REVERT: A 175 LYS cc_start: 0.7279 (pttm) cc_final: 0.6279 (pttt) REVERT: A 214 GLU cc_start: 0.8118 (pm20) cc_final: 0.7897 (pm20) REVERT: A 241 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7321 (ttm170) REVERT: C 28 ILE cc_start: 0.8641 (mm) cc_final: 0.8177 (tp) REVERT: C 175 LYS cc_start: 0.7311 (pttm) cc_final: 0.6295 (pttt) REVERT: C 241 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7433 (ttm170) REVERT: D 25 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7433 (mm) outliers start: 17 outliers final: 5 residues processed: 123 average time/residue: 0.5711 time to fit residues: 73.8685 Evaluate side-chains 118 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 241 ARG Chi-restraints excluded: chain D residue 25 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.186708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.134361 restraints weight = 7012.909| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.74 r_work: 0.3347 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7096 Z= 0.142 Angle : 0.536 5.120 9554 Z= 0.263 Chirality : 0.036 0.124 1130 Planarity : 0.004 0.038 1042 Dihedral : 14.541 124.933 2198 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.01 % Allowed : 17.47 % Favored : 79.52 % 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: 3.38 (0.29), residues: 752 helix: 3.01 (0.20), residues: 568 sheet: None (None), residues: 0 loop : -0.38 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 146 TYR 0.015 0.002 TYR A 123 PHE 0.015 0.001 PHE A 127 TRP 0.011 0.001 TRP A 220 HIS 0.002 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 7080) covalent geometry : angle 0.53567 / 0.26 ( 9550) SS BOND : bond 0.00716 / 0.36 ( 2) SS BOND : angle 0.56291 / 0.33 ( 4) hydrogen bonds : bond 0.06001 / 4.23 ( 442) hydrogen bonds : angle 3.42385 / 2.48 ( 1320) Misc. bond : bond 0.00028 / 0.02 ( 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 141 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ILE cc_start: 0.8560 (mm) cc_final: 0.7886 (tp) REVERT: A 44 ARG cc_start: 0.7078 (mtm110) cc_final: 0.6787 (mtm110) REVERT: A 154 MET cc_start: 0.8141 (mmt) cc_final: 0.7738 (mmm) REVERT: A 174 ARG cc_start: 0.7510 (mtp-110) cc_final: 0.7302 (mtp85) REVERT: A 175 LYS cc_start: 0.7271 (pttm) cc_final: 0.6261 (pttt) REVERT: A 214 GLU cc_start: 0.8119 (pm20) cc_final: 0.7899 (pm20) REVERT: C 28 ILE cc_start: 0.8599 (mm) cc_final: 0.7931 (tp) REVERT: C 154 MET cc_start: 0.8204 (mmt) cc_final: 0.7828 (mmm) REVERT: C 175 LYS cc_start: 0.7305 (pttm) cc_final: 0.6280 (pttt) REVERT: C 241 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7464 (ttm170) REVERT: D 25 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7442 (mm) outliers start: 20 outliers final: 5 residues processed: 134 average time/residue: 0.5086 time to fit residues: 71.9393 Evaluate side-chains 122 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 241 ARG Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain D residue 25 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 0.0010 chunk 70 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 65 optimal weight: 0.0470 chunk 50 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 overall best weight: 0.5284 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.189467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.137718 restraints weight = 6991.768| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.72 r_work: 0.3416 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7096 Z= 0.114 Angle : 0.505 5.918 9554 Z= 0.248 Chirality : 0.034 0.142 1130 Planarity : 0.004 0.037 1042 Dihedral : 14.196 123.931 2198 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.20 % Allowed : 20.03 % 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 are not related in a simple way. whole: 3.58 (0.29), residues: 752 helix: 3.22 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -0.50 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 146 TYR 0.016 0.001 TYR A 326 PHE 0.012 0.001 PHE A 127 TRP 0.008 0.001 TRP C 220 HIS 0.001 0.001 HIS C 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 ( 7080) covalent geometry : angle 0.50501 / 0.25 ( 9550) SS BOND : bond 0.00886 / 0.44 ( 2) SS BOND : angle 1.13352 / 0.56 ( 4) hydrogen bonds : bond 0.05102 / 3.63 ( 442) hydrogen bonds : angle 3.28324 / 2.38 ( 1320) Misc. bond : bond 0.00017 / 0.01 ( 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 119 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LEU cc_start: 0.7727 (mt) cc_final: 0.7443 (mm) REVERT: A 28 ILE cc_start: 0.8537 (mm) cc_final: 0.8119 (tp) REVERT: A 154 MET cc_start: 0.8162 (mmt) cc_final: 0.7742 (mmm) REVERT: A 174 ARG cc_start: 0.7451 (mtp-110) cc_final: 0.7244 (mtp85) REVERT: A 175 LYS cc_start: 0.7257 (pttm) cc_final: 0.6332 (pttp) REVERT: A 214 GLU cc_start: 0.8111 (pm20) cc_final: 0.7893 (pm20) REVERT: C 28 ILE cc_start: 0.8568 (mm) cc_final: 0.8138 (tp) REVERT: C 154 MET cc_start: 0.8136 (mmt) cc_final: 0.7741 (mmm) REVERT: C 175 LYS cc_start: 0.7302 (pttm) cc_final: 0.6379 (pttp) REVERT: D 25 LEU cc_start: 0.7752 (mt) cc_final: 0.7414 (mm) outliers start: 8 outliers final: 5 residues processed: 115 average time/residue: 0.4719 time to fit residues: 57.1916 Evaluate side-chains 113 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 179 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.189073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.137131 restraints weight = 6947.420| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.73 r_work: 0.3409 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7096 Z= 0.124 Angle : 0.513 5.209 9554 Z= 0.251 Chirality : 0.035 0.125 1130 Planarity : 0.004 0.037 1042 Dihedral : 14.232 123.454 2198 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.66 % Allowed : 20.03 % Favored : 78.31 % 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: 3.60 (0.29), residues: 752 helix: 3.25 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -0.54 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 146 TYR 0.014 0.001 TYR A 123 PHE 0.014 0.001 PHE A 127 TRP 0.010 0.001 TRP C 220 HIS 0.002 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 7080) covalent geometry : angle 0.51311 / 0.25 ( 9550) SS BOND : bond 0.00816 / 0.41 ( 2) SS BOND : angle 0.69788 / 0.35 ( 4) hydrogen bonds : bond 0.05350 / 3.80 ( 442) hydrogen bonds : angle 3.29775 / 2.38 ( 1320) Misc. bond : bond 0.00020 / 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 117 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LEU cc_start: 0.7825 (mt) cc_final: 0.7530 (mm) REVERT: A 28 ILE cc_start: 0.8587 (mm) cc_final: 0.8175 (tp) REVERT: A 154 MET cc_start: 0.8177 (mmt) cc_final: 0.7755 (mmm) REVERT: A 174 ARG cc_start: 0.7444 (mtp-110) cc_final: 0.7228 (mtp85) REVERT: A 175 LYS cc_start: 0.7301 (pttm) cc_final: 0.6383 (pttp) REVERT: A 214 GLU cc_start: 0.8122 (pm20) cc_final: 0.7884 (pm20) REVERT: C 28 ILE cc_start: 0.8592 (mm) cc_final: 0.8168 (tp) REVERT: C 154 MET cc_start: 0.8211 (mmt) cc_final: 0.7823 (mmm) REVERT: C 175 LYS cc_start: 0.7424 (pttm) cc_final: 0.6374 (pttp) REVERT: D 25 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7465 (mm) outliers start: 11 outliers final: 7 residues processed: 113 average time/residue: 0.4630 time to fit residues: 55.0726 Evaluate side-chains 113 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain D residue 25 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 70 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.190253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.138669 restraints weight = 7006.987| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.74 r_work: 0.3423 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7096 Z= 0.121 Angle : 0.521 8.782 9554 Z= 0.252 Chirality : 0.035 0.125 1130 Planarity : 0.004 0.038 1042 Dihedral : 14.204 123.271 2198 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.66 % Allowed : 20.33 % Favored : 78.01 % 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: 3.61 (0.29), residues: 752 helix: 3.26 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -0.56 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 146 TYR 0.016 0.001 TYR C 326 PHE 0.013 0.001 PHE C 127 TRP 0.009 0.001 TRP A 220 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 7080) covalent geometry : angle 0.52106 / 0.25 ( 9550) SS BOND : bond 0.00697 / 0.35 ( 2) SS BOND : angle 0.69993 / 0.35 ( 4) hydrogen bonds : bond 0.05249 / 3.73 ( 442) hydrogen bonds : angle 3.27610 / 2.37 ( 1320) Misc. bond : bond 0.00018 / 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 121 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LEU cc_start: 0.7793 (mt) cc_final: 0.7491 (mm) REVERT: A 28 ILE cc_start: 0.8519 (mm) cc_final: 0.8087 (tp) REVERT: A 154 MET cc_start: 0.8129 (mmt) cc_final: 0.7737 (mmm) REVERT: A 174 ARG cc_start: 0.7447 (mtp-110) cc_final: 0.7228 (mtp85) REVERT: A 175 LYS cc_start: 0.7252 (pttm) cc_final: 0.6328 (pttp) REVERT: A 214 GLU cc_start: 0.8142 (pm20) cc_final: 0.7905 (pm20) REVERT: A 241 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7329 (ttm170) REVERT: C 28 ILE cc_start: 0.8528 (mm) cc_final: 0.8109 (tp) REVERT: C 154 MET cc_start: 0.8173 (mmt) cc_final: 0.7780 (mmm) REVERT: C 175 LYS cc_start: 0.7453 (pttm) cc_final: 0.6392 (pttp) REVERT: D 25 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7416 (mm) outliers start: 11 outliers final: 8 residues processed: 117 average time/residue: 0.5324 time to fit residues: 65.6331 Evaluate side-chains 118 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain D residue 25 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 65 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.188887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.136894 restraints weight = 7008.337| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.75 r_work: 0.3416 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7096 Z= 0.125 Angle : 0.524 7.317 9554 Z= 0.254 Chirality : 0.035 0.126 1130 Planarity : 0.004 0.038 1042 Dihedral : 14.186 123.170 2198 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.81 % Allowed : 19.58 % Favored : 78.61 % 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: 3.58 (0.30), residues: 752 helix: 3.25 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -0.60 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 146 TYR 0.014 0.002 TYR A 123 PHE 0.014 0.001 PHE C 127 TRP 0.010 0.001 TRP C 220 HIS 0.003 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 7080) covalent geometry : angle 0.52383 / 0.25 ( 9550) SS BOND : bond 0.00737 / 0.37 ( 2) SS BOND : angle 0.64412 / 0.32 ( 4) hydrogen bonds : bond 0.05373 / 3.81 ( 442) hydrogen bonds : angle 3.29830 / 2.38 ( 1320) Misc. bond : bond 0.00018 / 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 122 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LEU cc_start: 0.7908 (mt) cc_final: 0.7587 (mm) REVERT: A 28 ILE cc_start: 0.8536 (mm) cc_final: 0.8163 (tp) REVERT: A 154 MET cc_start: 0.8155 (mmt) cc_final: 0.7761 (mmm) REVERT: A 174 ARG cc_start: 0.7501 (mtp-110) cc_final: 0.7275 (mtp85) REVERT: A 175 LYS cc_start: 0.7424 (pttm) cc_final: 0.6355 (pttp) REVERT: A 214 GLU cc_start: 0.8145 (pm20) cc_final: 0.7907 (pm20) REVERT: A 241 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7305 (ttm170) REVERT: C 28 ILE cc_start: 0.8503 (mm) cc_final: 0.8131 (tp) REVERT: C 154 MET cc_start: 0.8182 (mmt) cc_final: 0.7790 (mmm) REVERT: C 175 LYS cc_start: 0.7445 (pttm) cc_final: 0.6397 (pttp) REVERT: D 25 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7473 (mm) outliers start: 12 outliers final: 9 residues processed: 116 average time/residue: 0.5167 time to fit residues: 63.0648 Evaluate side-chains 120 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain D residue 25 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 36 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 25 optimal weight: 0.4980 chunk 54 optimal weight: 0.0970 chunk 53 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 269 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.190001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.138433 restraints weight = 6946.050| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.74 r_work: 0.3450 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7096 Z= 0.118 Angle : 0.518 8.119 9554 Z= 0.250 Chirality : 0.034 0.125 1130 Planarity : 0.004 0.038 1042 Dihedral : 14.025 122.758 2198 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.26 % Allowed : 19.28 % Favored : 78.46 % 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: 3.63 (0.30), residues: 752 helix: 3.28 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -0.59 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 146 TYR 0.016 0.002 TYR C 326 PHE 0.013 0.001 PHE C 127 TRP 0.009 0.001 TRP C 220 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 ( 7080) covalent geometry : angle 0.51733 / 0.25 ( 9550) SS BOND : bond 0.00498 / 0.25 ( 2) SS BOND : angle 0.97209 / 0.49 ( 4) hydrogen bonds : bond 0.05125 / 3.65 ( 442) hydrogen bonds : angle 3.25503 / 2.35 ( 1320) Misc. bond : bond 0.00016 / 0.01 ( 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 124 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LEU cc_start: 0.7888 (mt) cc_final: 0.7562 (mm) REVERT: A 28 ILE cc_start: 0.8490 (mm) cc_final: 0.8092 (tp) REVERT: A 154 MET cc_start: 0.8087 (mmt) cc_final: 0.7712 (mmm) REVERT: A 174 ARG cc_start: 0.7489 (mtp-110) cc_final: 0.7263 (mtp85) REVERT: A 175 LYS cc_start: 0.7408 (pttm) cc_final: 0.6345 (pttp) REVERT: A 214 GLU cc_start: 0.8159 (pm20) cc_final: 0.7898 (pm20) REVERT: A 241 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7314 (ttm170) REVERT: C 28 ILE cc_start: 0.8478 (mm) cc_final: 0.8084 (tp) REVERT: C 154 MET cc_start: 0.8081 (mmt) cc_final: 0.7710 (mmm) REVERT: C 175 LYS cc_start: 0.7446 (pttm) cc_final: 0.6373 (pttp) REVERT: D 25 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7465 (mm) outliers start: 15 outliers final: 9 residues processed: 118 average time/residue: 0.5202 time to fit residues: 64.8568 Evaluate side-chains 121 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain D residue 25 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 20 optimal weight: 0.0570 chunk 65 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 56 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.0770 chunk 63 optimal weight: 1.9990 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.193111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.142175 restraints weight = 6972.420| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.73 r_work: 0.3495 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7096 Z= 0.105 Angle : 0.507 9.150 9554 Z= 0.241 Chirality : 0.033 0.125 1130 Planarity : 0.004 0.037 1042 Dihedral : 13.697 122.019 2198 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.66 % Allowed : 20.03 % Favored : 78.31 % 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: 3.76 (0.30), residues: 752 helix: 3.33 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -0.51 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 146 TYR 0.014 0.001 TYR A 76 PHE 0.010 0.001 PHE C 127 TRP 0.007 0.001 TRP D 26 HIS 0.001 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.11 ( 7080) covalent geometry : angle 0.50657 / 0.24 ( 9550) SS BOND : bond 0.00339 / 0.17 ( 2) SS BOND : angle 1.03603 / 0.53 ( 4) hydrogen bonds : bond 0.04492 / 3.22 ( 442) hydrogen bonds : angle 3.16617 / 2.29 ( 1320) Misc. bond : bond 0.00012 / 0.01 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2471.93 seconds wall clock time: 42 minutes 47.64 seconds (2567.64 seconds total)