Starting phenix.real_space_refine on Tue Aug 4 17:46:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wdi_65890/08_2026/9wdi_65890.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wdi_65890/08_2026/9wdi_65890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wdi_65890/08_2026/9wdi_65890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wdi_65890/08_2026/9wdi_65890.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wdi_65890/08_2026/9wdi_65890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wdi_65890/08_2026/9wdi_65890.map" } resolution = 3.33 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= 0.012 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 3606 2.51 5 N 960 2.21 5 O 898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5504 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2157 Classifications: {'peptide': 277} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 261} Chain: "B" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 595 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "C" Number of atoms: 2157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2157 Classifications: {'peptide': 277} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 261} Chain: "D" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 595 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 69} Time building chain proxies: 1.58, per 1000 atoms: 0.29 Number of scatterers: 5504 At special positions: 0 Unit cell: (91.632, 62.416, 107.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 898 8.00 N 960 7.00 C 3606 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS C 313 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 50 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 57 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 58 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 50 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 57 " distance=2.03 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 58 " 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=0, symmetry=0 Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 200.1 milliseconds 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1304 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 2 sheets defined 83.6% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 38 through 69 Proline residue: A 57 - end of helix Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 76 through 102 Proline residue: A 94 - end of helix Proline residue: A 99 - end of helix Processing helix chain 'A' and resid 109 through 144 removed outlier: 3.739A pdb=" N TRP A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER A 117 " --> pdb=" O CYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 148 removed outlier: 3.782A pdb=" N LYS A 148 " --> pdb=" O PRO A 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 145 through 148' Processing helix chain 'A' and resid 150 through 178 removed outlier: 3.601A pdb=" N THR A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP A 165 " --> pdb=" O GLN A 161 " (cutoff:3.500A) Proline residue: A 174 - end of helix Processing helix chain 'A' and resid 199 through 215 Processing helix chain 'A' and resid 215 through 233 Processing helix chain 'A' and resid 237 through 264 Proline residue: A 254 - end of helix Processing helix chain 'A' and resid 269 through 301 Proline residue: A 280 - end of helix removed outlier: 4.273A pdb=" N SER A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Proline residue: A 294 - end of helix Processing helix chain 'A' and resid 301 through 314 Processing helix chain 'B' and resid 4 through 15 Processing helix chain 'B' and resid 18 through 29 removed outlier: 3.547A pdb=" N LYS B 22 " --> pdb=" O HIS B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 42 Processing helix chain 'B' and resid 47 through 67 removed outlier: 3.963A pdb=" N GLU B 67 " --> pdb=" O LYS B 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 69 Proline residue: C 57 - end of helix Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 76 through 102 Proline residue: C 94 - end of helix Proline residue: C 99 - end of helix Processing helix chain 'C' and resid 109 through 144 removed outlier: 3.612A pdb=" N TRP C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER C 117 " --> pdb=" O CYS C 113 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER C 118 " --> pdb=" O TRP C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 148 removed outlier: 3.770A pdb=" N LYS C 148 " --> pdb=" O PRO C 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 145 through 148' Processing helix chain 'C' and resid 150 through 178 removed outlier: 3.671A pdb=" N THR C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRP C 165 " --> pdb=" O GLN C 161 " (cutoff:3.500A) Proline residue: C 174 - end of helix Processing helix chain 'C' and resid 199 through 215 Processing helix chain 'C' and resid 215 through 233 Processing helix chain 'C' and resid 237 through 264 Proline residue: C 254 - end of helix Processing helix chain 'C' and resid 269 through 301 Proline residue: C 280 - end of helix removed outlier: 4.253A pdb=" N SER C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Proline residue: C 294 - end of helix Processing helix chain 'C' and resid 301 through 314 Processing helix chain 'D' and resid 4 through 15 Processing helix chain 'D' and resid 18 through 29 removed outlier: 3.547A pdb=" N LYS D 22 " --> pdb=" O HIS D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 42 Processing helix chain 'D' and resid 47 through 67 removed outlier: 3.972A pdb=" N GLU D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 184 Processing sheet with id=AA2, first strand: chain 'C' and resid 179 through 184 removed outlier: 3.570A pdb=" N GLY C 193 " --> pdb=" O ARG C 180 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1257 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: 0.84 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1718 1.35 - 1.46: 1405 1.46 - 1.58: 2485 1.58 - 1.70: 0 1.70 - 1.82: 52 Bond restraints: 5660 Sorted by residual: bond pdb=" C LEU C 93 " pdb=" N PRO C 94 " ideal model delta sigma weight residual 1.335 1.357 -0.021 1.36e-02 5.41e+03 2.45e+00 bond pdb=" C LEU A 93 " pdb=" N PRO A 94 " ideal model delta sigma weight residual 1.335 1.356 -0.020 1.36e-02 5.41e+03 2.22e+00 bond pdb=" CB ILE C 121 " pdb=" CG2 ILE C 121 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.64e+00 bond pdb=" CB ILE A 121 " pdb=" CG2 ILE A 121 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.52e+00 bond pdb=" CD2 TYR C 125 " pdb=" CE2 TYR C 125 " ideal model delta sigma weight residual 1.382 1.349 0.033 3.00e-02 1.11e+03 1.23e+00 ... (remaining 5655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 7232 0.99 - 1.99: 367 1.99 - 2.98: 74 2.98 - 3.97: 11 3.97 - 4.96: 22 Bond angle restraints: 7706 Sorted by residual: angle pdb=" C VAL A 173 " pdb=" CA VAL A 173 " pdb=" CB VAL A 173 " ideal model delta sigma weight residual 113.70 110.72 2.98 9.50e-01 1.11e+00 9.83e+00 angle pdb=" C VAL C 173 " pdb=" CA VAL C 173 " pdb=" CB VAL C 173 " ideal model delta sigma weight residual 113.70 110.82 2.88 9.50e-01 1.11e+00 9.21e+00 angle pdb=" C THR A 172 " pdb=" N VAL A 173 " pdb=" CA VAL A 173 " ideal model delta sigma weight residual 120.43 122.94 -2.51 9.60e-01 1.09e+00 6.84e+00 angle pdb=" C THR C 172 " pdb=" N VAL C 173 " pdb=" CA VAL C 173 " ideal model delta sigma weight residual 120.43 122.89 -2.46 9.60e-01 1.09e+00 6.58e+00 angle pdb=" C ALA C 142 " pdb=" N PHE C 143 " pdb=" CA PHE C 143 " ideal model delta sigma weight residual 121.81 117.70 4.11 1.83e+00 2.99e-01 5.04e+00 ... (remaining 7701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.52: 2988 14.52 - 29.03: 266 29.03 - 43.55: 64 43.55 - 58.07: 8 58.07 - 72.58: 10 Dihedral angle restraints: 3336 sinusoidal: 1310 harmonic: 2026 Sorted by residual: dihedral pdb=" CB CYS D 24 " pdb=" SG CYS D 24 " pdb=" SG CYS D 50 " pdb=" CB CYS D 50 " ideal model delta sinusoidal sigma weight residual 93.00 56.88 36.12 1 1.00e+01 1.00e-02 1.84e+01 dihedral pdb=" CB CYS B 24 " pdb=" SG CYS B 24 " pdb=" SG CYS B 50 " pdb=" CB CYS B 50 " ideal model delta sinusoidal sigma weight residual 93.00 56.89 36.11 1 1.00e+01 1.00e-02 1.84e+01 dihedral pdb=" CB CYS A 313 " pdb=" SG CYS A 313 " pdb=" SG CYS C 306 " pdb=" CB CYS C 306 " ideal model delta sinusoidal sigma weight residual -86.00 -121.32 35.32 1 1.00e+01 1.00e-02 1.77e+01 ... (remaining 3333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 471 0.023 - 0.046: 224 0.046 - 0.069: 115 0.069 - 0.092: 36 0.092 - 0.115: 32 Chirality restraints: 878 Sorted by residual: chirality pdb=" CA PRO C 174 " pdb=" N PRO C 174 " pdb=" C PRO C 174 " pdb=" CB PRO C 174 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.30e-01 chirality pdb=" CA PRO C 280 " pdb=" N PRO C 280 " pdb=" C PRO C 280 " pdb=" CB PRO C 280 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.22e-01 chirality pdb=" CA THR A 253 " pdb=" N THR A 253 " pdb=" C THR A 253 " pdb=" CB THR A 253 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.11 2.00e-01 2.50e+01 3.10e-01 ... (remaining 875 not shown) Planarity restraints: 952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 217 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.36e+00 pdb=" N PRO A 218 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 218 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 218 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 217 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO C 218 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 218 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 218 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 106 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO A 107 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 107 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 107 " 0.021 5.00e-02 4.00e+02 ... (remaining 949 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 1869 2.87 - 3.38: 5697 3.38 - 3.89: 9279 3.89 - 4.39: 9683 4.39 - 4.90: 17452 Nonbonded interactions: 43980 Sorted by model distance: nonbonded pdb=" O TRP C 67 " pdb=" OG SER C 70 " model vdw 2.368 3.040 nonbonded pdb=" O TRP A 67 " pdb=" OG SER A 70 " model vdw 2.377 3.040 nonbonded pdb=" NH2 ARG C 179 " pdb=" OXT GLY D 76 " model vdw 2.405 3.120 nonbonded pdb=" NH2 ARG A 179 " pdb=" OXT GLY B 76 " model vdw 2.416 3.120 nonbonded pdb=" NH2 ARG A 259 " pdb=" O LEU B 75 " model vdw 2.417 3.120 ... (remaining 43975 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' selection = chain 'C' } 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: 0.650 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.120 Find NCS groups from input model: 0.080 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5670 Z= 0.154 Angle : 0.559 4.965 7726 Z= 0.309 Chirality : 0.038 0.115 878 Planarity : 0.005 0.046 952 Dihedral : 12.096 72.583 2002 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.37 (0.32), residues: 694 helix: 2.27 (0.22), residues: 548 sheet: -2.77 (0.94), residues: 20 loop : -0.86 (0.49), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 179 TYR 0.019 0.002 TYR A 125 PHE 0.015 0.002 PHE C 143 TRP 0.015 0.001 TRP A 114 HIS 0.003 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 5660) covalent geometry : angle 0.55691 / 0.31 ( 7706) SS BOND : bond 0.00197 / 0.12 ( 10) SS BOND : angle 1.00068 / 0.61 ( 20) hydrogen bonds : bond 0.11444 / 6.97 ( 421) hydrogen bonds : angle 4.83000 / 3.63 ( 1257) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.247 Fit side-chains REVERT: A 180 ARG cc_start: 0.5374 (mmt180) cc_final: 0.5029 (mtp-110) REVERT: A 238 TRP cc_start: 0.5631 (t60) cc_final: 0.5299 (t-100) REVERT: A 296 MET cc_start: 0.7315 (ttm) cc_final: 0.7100 (ttp) REVERT: A 304 GLN cc_start: 0.6364 (tp40) cc_final: 0.5938 (tt0) REVERT: C 296 MET cc_start: 0.7316 (ttm) cc_final: 0.7101 (ttp) REVERT: C 304 GLN cc_start: 0.6185 (tp40) cc_final: 0.5635 (tt0) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1169 time to fit residues: 21.2461 Evaluate side-chains 118 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4350 r_free = 0.4350 target = 0.195164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.153275 restraints weight = 6534.077| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.06 r_work: 0.3844 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5670 Z= 0.162 Angle : 0.630 7.772 7726 Z= 0.313 Chirality : 0.042 0.127 878 Planarity : 0.005 0.043 952 Dihedral : 3.729 20.764 766 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.89 % Allowed : 10.82 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.28 (0.31), residues: 694 helix: 2.22 (0.22), residues: 550 sheet: -1.76 (0.98), residues: 20 loop : -1.22 (0.47), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 179 TYR 0.011 0.001 TYR A 125 PHE 0.014 0.002 PHE B 54 TRP 0.014 0.001 TRP A 78 HIS 0.004 0.001 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 5660) covalent geometry : angle 0.62777 / 0.31 ( 7706) SS BOND : bond 0.00338 / 0.20 ( 10) SS BOND : angle 1.23294 / 0.74 ( 20) hydrogen bonds : bond 0.04749 / 3.25 ( 421) hydrogen bonds : angle 4.34402 / 3.23 ( 1257) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.208 Fit side-chains REVERT: A 158 ARG cc_start: 0.8318 (mtp-110) cc_final: 0.8090 (ptm-80) REVERT: A 161 GLN cc_start: 0.7592 (mt0) cc_final: 0.7315 (mt0) REVERT: A 180 ARG cc_start: 0.5187 (mmt180) cc_final: 0.4460 (mtp-110) REVERT: A 238 TRP cc_start: 0.5559 (t60) cc_final: 0.4865 (t-100) REVERT: A 304 GLN cc_start: 0.6430 (tp40) cc_final: 0.5691 (tt0) REVERT: C 161 GLN cc_start: 0.7717 (mt0) cc_final: 0.7353 (mt0) REVERT: C 304 GLN cc_start: 0.6441 (tp40) cc_final: 0.5614 (tt0) outliers start: 11 outliers final: 11 residues processed: 109 average time/residue: 0.0964 time to fit residues: 12.9615 Evaluate side-chains 110 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 238 TRP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 73 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 46 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS C 226 HIS C 304 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.204799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.160628 restraints weight = 6674.891| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.20 r_work: 0.3810 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5670 Z= 0.137 Angle : 0.566 6.013 7726 Z= 0.286 Chirality : 0.040 0.114 878 Planarity : 0.005 0.044 952 Dihedral : 3.705 18.381 766 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.75 % Allowed : 11.17 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.41 (0.32), residues: 694 helix: 2.32 (0.22), residues: 550 sheet: -1.44 (0.98), residues: 20 loop : -1.29 (0.46), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 302 TYR 0.010 0.001 TYR C 125 PHE 0.013 0.001 PHE A 297 TRP 0.012 0.001 TRP A 64 HIS 0.012 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 5660) covalent geometry : angle 0.56535 / 0.29 ( 7706) SS BOND : bond 0.00163 / 0.10 ( 10) SS BOND : angle 0.90560 / 0.58 ( 20) hydrogen bonds : bond 0.04360 / 2.95 ( 421) hydrogen bonds : angle 4.26596 / 3.17 ( 1257) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.221 Fit side-chains REVERT: A 161 GLN cc_start: 0.7463 (mt0) cc_final: 0.7151 (mt0) REVERT: A 180 ARG cc_start: 0.5209 (mmt180) cc_final: 0.4509 (mtp-110) REVERT: A 238 TRP cc_start: 0.5676 (t60) cc_final: 0.4856 (t-100) REVERT: A 304 GLN cc_start: 0.6409 (tp40) cc_final: 0.5636 (tt0) REVERT: C 161 GLN cc_start: 0.7452 (mt0) cc_final: 0.7131 (mt0) REVERT: C 304 GLN cc_start: 0.6344 (tp-100) cc_final: 0.5495 (tt0) outliers start: 16 outliers final: 15 residues processed: 110 average time/residue: 0.0997 time to fit residues: 13.5121 Evaluate side-chains 125 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 238 TRP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 73 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 0.0870 chunk 26 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS C 226 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.196271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.154016 restraints weight = 6464.054| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.05 r_work: 0.3818 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5670 Z= 0.145 Angle : 0.564 5.048 7726 Z= 0.285 Chirality : 0.040 0.115 878 Planarity : 0.005 0.043 952 Dihedral : 3.737 21.947 766 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.92 % Allowed : 12.03 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.40 (0.32), residues: 694 helix: 2.34 (0.22), residues: 550 sheet: -1.34 (0.93), residues: 20 loop : -1.44 (0.45), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 302 TYR 0.008 0.001 TYR A 125 PHE 0.013 0.001 PHE C 297 TRP 0.015 0.001 TRP A 64 HIS 0.003 0.001 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 5660) covalent geometry : angle 0.56287 / 0.29 ( 7706) SS BOND : bond 0.00176 / 0.11 ( 10) SS BOND : angle 0.84372 / 0.55 ( 20) hydrogen bonds : bond 0.04288 / 2.91 ( 421) hydrogen bonds : angle 4.19120 / 3.12 ( 1257) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.206 Fit side-chains REVERT: A 64 TRP cc_start: 0.8127 (t-100) cc_final: 0.7854 (t-100) REVERT: A 68 LYS cc_start: 0.5814 (mmtt) cc_final: 0.4907 (mmtm) REVERT: A 161 GLN cc_start: 0.7474 (mt0) cc_final: 0.7166 (mt0) REVERT: A 304 GLN cc_start: 0.6598 (tp40) cc_final: 0.5759 (tt0) REVERT: C 64 TRP cc_start: 0.8166 (t-100) cc_final: 0.7886 (t-100) REVERT: C 68 LYS cc_start: 0.5829 (mmtt) cc_final: 0.4913 (mmtm) REVERT: C 161 GLN cc_start: 0.7458 (mt0) cc_final: 0.7137 (mt0) REVERT: C 304 GLN cc_start: 0.6301 (tp-100) cc_final: 0.5554 (tt0) outliers start: 17 outliers final: 17 residues processed: 114 average time/residue: 0.0856 time to fit residues: 12.3123 Evaluate side-chains 125 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 238 TRP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 73 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 0.0010 chunk 31 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.0020 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS A 304 GLN C 226 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.198158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.156625 restraints weight = 6556.991| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.01 r_work: 0.3851 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5670 Z= 0.124 Angle : 0.560 9.642 7726 Z= 0.275 Chirality : 0.039 0.113 878 Planarity : 0.005 0.042 952 Dihedral : 3.719 22.310 766 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.92 % Allowed : 13.40 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.55 (0.32), residues: 694 helix: 2.45 (0.22), residues: 550 sheet: -0.98 (0.90), residues: 20 loop : -1.50 (0.45), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 302 TYR 0.008 0.001 TYR A 125 PHE 0.013 0.001 PHE D 33 TRP 0.011 0.001 TRP A 64 HIS 0.003 0.001 HIS C 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 5660) covalent geometry : angle 0.55920 / 0.28 ( 7706) SS BOND : bond 0.00151 / 0.10 ( 10) SS BOND : angle 0.77510 / 0.52 ( 20) hydrogen bonds : bond 0.03942 / 2.69 ( 421) hydrogen bonds : angle 4.09074 / 3.05 ( 1257) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.262 Fit side-chains REVERT: A 161 GLN cc_start: 0.7430 (mt0) cc_final: 0.7127 (mt0) REVERT: A 228 ILE cc_start: 0.7177 (mt) cc_final: 0.6921 (mt) REVERT: A 304 GLN cc_start: 0.6479 (tp-100) cc_final: 0.5663 (tt0) REVERT: C 64 TRP cc_start: 0.8146 (t-100) cc_final: 0.7933 (t-100) REVERT: C 68 LYS cc_start: 0.5764 (mmtt) cc_final: 0.5531 (mmmt) REVERT: C 161 GLN cc_start: 0.7403 (mt0) cc_final: 0.7096 (mt0) REVERT: C 304 GLN cc_start: 0.6341 (tp-100) cc_final: 0.5558 (tt0) REVERT: D 6 ARG cc_start: 0.8344 (ptm160) cc_final: 0.7955 (ptm160) outliers start: 17 outliers final: 14 residues processed: 122 average time/residue: 0.0825 time to fit residues: 12.8243 Evaluate side-chains 124 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 238 TRP Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 73 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 27 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 0 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS C 226 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.205282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.161162 restraints weight = 6702.457| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.19 r_work: 0.3816 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5670 Z= 0.142 Angle : 0.585 8.786 7726 Z= 0.290 Chirality : 0.040 0.115 878 Planarity : 0.005 0.043 952 Dihedral : 3.809 23.300 766 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.95 % Allowed : 13.75 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.48 (0.31), residues: 694 helix: 2.39 (0.22), residues: 550 sheet: -0.83 (0.92), residues: 20 loop : -1.51 (0.46), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 30 TYR 0.011 0.001 TYR C 186 PHE 0.013 0.001 PHE B 33 TRP 0.021 0.002 TRP C 78 HIS 0.004 0.001 HIS C 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 5660) covalent geometry : angle 0.58408 / 0.29 ( 7706) SS BOND : bond 0.00163 / 0.11 ( 10) SS BOND : angle 0.80584 / 0.54 ( 20) hydrogen bonds : bond 0.04139 / 2.81 ( 421) hydrogen bonds : angle 4.13307 / 3.09 ( 1257) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.196 Fit side-chains REVERT: A 304 GLN cc_start: 0.6469 (tp-100) cc_final: 0.5705 (tt0) REVERT: C 64 TRP cc_start: 0.8118 (t-100) cc_final: 0.7884 (t-100) REVERT: C 304 GLN cc_start: 0.6358 (tp-100) cc_final: 0.5579 (tt0) REVERT: D 6 ARG cc_start: 0.8288 (ptm160) cc_final: 0.7892 (ptm160) outliers start: 23 outliers final: 20 residues processed: 119 average time/residue: 0.0910 time to fit residues: 13.6813 Evaluate side-chains 134 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 238 TRP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 73 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS C 226 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.204617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.160388 restraints weight = 6779.582| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.22 r_work: 0.3805 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5670 Z= 0.149 Angle : 0.601 8.356 7726 Z= 0.301 Chirality : 0.040 0.113 878 Planarity : 0.005 0.043 952 Dihedral : 3.893 23.808 766 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.95 % Allowed : 14.09 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.44 (0.32), residues: 694 helix: 2.35 (0.22), residues: 550 sheet: -0.64 (0.93), residues: 20 loop : -1.48 (0.47), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 302 TYR 0.019 0.002 TYR A 186 PHE 0.013 0.001 PHE B 33 TRP 0.034 0.002 TRP A 78 HIS 0.004 0.001 HIS C 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 5660) covalent geometry : angle 0.60009 / 0.30 ( 7706) SS BOND : bond 0.00186 / 0.12 ( 10) SS BOND : angle 0.80795 / 0.54 ( 20) hydrogen bonds : bond 0.04211 / 2.87 ( 421) hydrogen bonds : angle 4.12784 / 3.08 ( 1257) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.177 Fit side-chains REVERT: A 158 ARG cc_start: 0.8424 (mtp-110) cc_final: 0.8003 (ptm-80) REVERT: A 304 GLN cc_start: 0.6557 (tp-100) cc_final: 0.5765 (tt0) REVERT: C 304 GLN cc_start: 0.6372 (tp-100) cc_final: 0.5595 (tt0) REVERT: D 6 ARG cc_start: 0.8263 (ptm160) cc_final: 0.8019 (ptt180) outliers start: 23 outliers final: 19 residues processed: 119 average time/residue: 0.0904 time to fit residues: 13.4888 Evaluate side-chains 133 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 73 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 40 optimal weight: 0.0670 chunk 58 optimal weight: 0.0070 chunk 30 optimal weight: 7.9990 chunk 3 optimal weight: 0.0370 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS A 237 HIS C 226 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.208052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.163491 restraints weight = 6725.341| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.24 r_work: 0.3881 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5670 Z= 0.120 Angle : 0.566 8.257 7726 Z= 0.284 Chirality : 0.039 0.112 878 Planarity : 0.004 0.042 952 Dihedral : 3.856 22.874 766 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.41 % Allowed : 14.78 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.64 (0.32), residues: 694 helix: 2.49 (0.22), residues: 550 sheet: -0.03 (1.01), residues: 20 loop : -1.54 (0.46), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 236 TYR 0.016 0.001 TYR A 186 PHE 0.013 0.001 PHE D 33 TRP 0.027 0.002 TRP A 78 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 5660) covalent geometry : angle 0.56575 / 0.28 ( 7706) SS BOND : bond 0.00154 / 0.10 ( 10) SS BOND : angle 0.73870 / 0.50 ( 20) hydrogen bonds : bond 0.03862 / 2.63 ( 421) hydrogen bonds : angle 4.02941 / 3.01 ( 1257) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.131 Fit side-chains REVERT: A 64 TRP cc_start: 0.7889 (t-100) cc_final: 0.7642 (t-100) REVERT: A 304 GLN cc_start: 0.6457 (tp-100) cc_final: 0.5732 (tt0) REVERT: C 304 GLN cc_start: 0.6254 (tp-100) cc_final: 0.5544 (tt0) outliers start: 14 outliers final: 13 residues processed: 104 average time/residue: 0.0855 time to fit residues: 10.9760 Evaluate side-chains 108 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 73 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 52 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 36 optimal weight: 0.0770 chunk 54 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS C 226 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.206135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.161449 restraints weight = 6718.938| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.21 r_work: 0.3854 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5670 Z= 0.136 Angle : 0.584 7.801 7726 Z= 0.292 Chirality : 0.040 0.113 878 Planarity : 0.004 0.042 952 Dihedral : 3.879 24.074 766 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.41 % Allowed : 15.12 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.60 (0.32), residues: 694 helix: 2.44 (0.22), residues: 550 sheet: 0.18 (1.06), residues: 20 loop : -1.51 (0.46), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 236 TYR 0.016 0.001 TYR A 186 PHE 0.012 0.001 PHE B 33 TRP 0.022 0.002 TRP A 78 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 5660) covalent geometry : angle 0.58310 / 0.29 ( 7706) SS BOND : bond 0.00173 / 0.11 ( 10) SS BOND : angle 0.78803 / 0.53 ( 20) hydrogen bonds : bond 0.04034 / 2.75 ( 421) hydrogen bonds : angle 4.04997 / 3.03 ( 1257) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.216 Fit side-chains REVERT: A 304 GLN cc_start: 0.6490 (tp-100) cc_final: 0.5770 (tt0) REVERT: C 304 GLN cc_start: 0.6289 (tp-100) cc_final: 0.5591 (tt0) outliers start: 14 outliers final: 14 residues processed: 104 average time/residue: 0.0881 time to fit residues: 11.5623 Evaluate side-chains 114 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 73 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS C 226 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.197773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.155694 restraints weight = 6599.946| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.07 r_work: 0.3862 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 5670 Z= 0.158 Angle : 0.658 11.004 7726 Z= 0.338 Chirality : 0.041 0.231 878 Planarity : 0.005 0.042 952 Dihedral : 4.290 24.726 766 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.41 % Allowed : 14.95 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.60 (0.32), residues: 694 helix: 2.50 (0.22), residues: 534 sheet: 0.24 (1.04), residues: 20 loop : -1.25 (0.43), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 302 TYR 0.015 0.001 TYR A 186 PHE 0.013 0.001 PHE D 33 TRP 0.028 0.002 TRP A 64 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 5660) covalent geometry : angle 0.63333 / 0.33 ( 7706) SS BOND : bond 0.00713 / 0.44 ( 10) SS BOND : angle 3.59536 / 3.02 ( 20) hydrogen bonds : bond 0.04376 / 2.98 ( 421) hydrogen bonds : angle 4.30300 / 3.17 ( 1257) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7936 (t-100) cc_final: 0.7687 (t-100) REVERT: A 180 ARG cc_start: 0.5008 (mmt180) cc_final: 0.4416 (mtp-110) REVERT: A 304 GLN cc_start: 0.6513 (tp-100) cc_final: 0.5783 (tt0) REVERT: C 304 GLN cc_start: 0.6316 (tp-100) cc_final: 0.5609 (tt0) outliers start: 14 outliers final: 14 residues processed: 105 average time/residue: 0.0891 time to fit residues: 11.7495 Evaluate side-chains 116 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 73 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS C 226 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.207048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.162902 restraints weight = 6725.344| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.20 r_work: 0.3874 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5670 Z= 0.138 Angle : 0.623 7.746 7726 Z= 0.315 Chirality : 0.040 0.179 878 Planarity : 0.005 0.042 952 Dihedral : 4.329 24.911 766 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.06 % Allowed : 15.29 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.61 (0.32), residues: 694 helix: 2.47 (0.22), residues: 546 sheet: 0.31 (1.03), residues: 20 loop : -1.48 (0.45), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 236 TYR 0.016 0.001 TYR A 186 PHE 0.016 0.001 PHE B 54 TRP 0.028 0.002 TRP C 64 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 5660) covalent geometry : angle 0.61125 / 0.31 ( 7706) SS BOND : bond 0.00522 / 0.32 ( 10) SS BOND : angle 2.47080 / 2.07 ( 20) hydrogen bonds : bond 0.04228 / 2.90 ( 421) hydrogen bonds : angle 4.19796 / 3.09 ( 1257) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1359.49 seconds wall clock time: 23 minutes 53.38 seconds (1433.38 seconds total)