Starting phenix.real_space_refine on Tue Aug 4 23:03:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gi9_40063/08_2026/8gi9_40063.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gi9_40063/08_2026/8gi9_40063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8gi9_40063/08_2026/8gi9_40063.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gi9_40063/08_2026/8gi9_40063.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gi9_40063/08_2026/8gi9_40063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gi9_40063/08_2026/8gi9_40063.map" model { file = "/net/cci-nas-00/data/ceres_data/8gi9_40063/08_2026/8gi9_40063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gi9_40063/08_2026/8gi9_40063.cif" } resolution = 2.84 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= 0.222 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 39 5.16 5 Na 9 4.78 5 C 4842 2.51 5 N 894 2.21 5 O 1062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 6852 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1948 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 12, 'TRANS': 227} Chain: "A" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 336 Unusual residues: {' NA': 3, 'CLR': 7, 'PEE': 2, 'RET': 1} Classifications: {'undetermined': 13, 'water': 15} Link IDs: {None: 27} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Restraints were copied for chains: B, C Time building chain proxies: 1.44, per 1000 atoms: 0.21 Number of scatterers: 6852 At special positions: 0 Unit cell: (79.31, 78.28, 76.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 6 15.00 Na 9 11.00 O 1062 8.00 N 894 7.00 C 4842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 331.2 milliseconds 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1326 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 79.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 21 through 48 removed outlier: 3.562A pdb=" N ASP A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 removed outlier: 3.523A pdb=" N ASN A 67 " --> pdb=" O PRO A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 68 through 90 removed outlier: 3.570A pdb=" N CYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.576A pdb=" N VAL A 107 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 109 through 122 Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 150 through 177 Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 181 through 199 removed outlier: 3.904A pdb=" N LEU A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.755A pdb=" N ILE A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'B' and resid 21 through 48 removed outlier: 3.562A pdb=" N ASP B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 67 removed outlier: 3.523A pdb=" N ASN B 67 " --> pdb=" O PRO B 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 64 through 67' Processing helix chain 'B' and resid 68 through 90 removed outlier: 3.570A pdb=" N CYS B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.576A pdb=" N VAL B 107 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 109 through 122 Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 150 through 177 Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 181 through 199 removed outlier: 3.904A pdb=" N LEU B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP B 190 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.755A pdb=" N ILE B 204 " --> pdb=" O PRO B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'C' and resid 21 through 48 removed outlier: 3.562A pdb=" N ASP C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 67 removed outlier: 3.522A pdb=" N ASN C 67 " --> pdb=" O PRO C 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 64 through 67' Processing helix chain 'C' and resid 68 through 90 removed outlier: 3.570A pdb=" N CYS C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.576A pdb=" N VAL C 107 " --> pdb=" O TYR C 103 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 108' Processing helix chain 'C' and resid 109 through 122 Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 150 through 177 Proline residue: C 164 - end of helix Processing helix chain 'C' and resid 181 through 199 removed outlier: 3.904A pdb=" N LEU C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP C 199 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.755A pdb=" N ILE C 204 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 Processing helix chain 'C' and resid 233 through 252 408 hydrogen bonds defined for protein. 1224 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: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1518 1.33 - 1.45: 1521 1.45 - 1.57: 3876 1.57 - 1.69: 114 1.69 - 1.81: 57 Bond restraints: 7086 Sorted by residual: bond pdb=" O4P PEE A 312 " pdb=" P PEE A 312 " ideal model delta sigma weight residual 1.653 1.786 -0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" O4P PEE B 312 " pdb=" P PEE B 312 " ideal model delta sigma weight residual 1.653 1.786 -0.133 2.00e-02 2.50e+03 4.39e+01 bond pdb=" O4P PEE C 312 " pdb=" P PEE C 312 " ideal model delta sigma weight residual 1.653 1.785 -0.132 2.00e-02 2.50e+03 4.39e+01 bond pdb=" O4P PEE B 313 " pdb=" P PEE B 313 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" O4P PEE A 313 " pdb=" P PEE A 313 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 9300 2.72 - 5.44: 318 5.44 - 8.15: 78 8.15 - 10.87: 3 10.87 - 13.59: 6 Bond angle restraints: 9705 Sorted by residual: angle pdb=" O1P PEE B 312 " pdb=" P PEE B 312 " pdb=" O2P PEE B 312 " ideal model delta sigma weight residual 119.43 133.02 -13.59 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1P PEE A 312 " pdb=" P PEE A 312 " pdb=" O2P PEE A 312 " ideal model delta sigma weight residual 119.43 133.01 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1P PEE C 312 " pdb=" P PEE C 312 " pdb=" O2P PEE C 312 " ideal model delta sigma weight residual 119.43 133.01 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1P PEE B 313 " pdb=" P PEE B 313 " pdb=" O2P PEE B 313 " ideal model delta sigma weight residual 119.43 133.01 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1P PEE A 313 " pdb=" P PEE A 313 " pdb=" O2P PEE A 313 " ideal model delta sigma weight residual 119.43 133.00 -13.57 3.00e+00 1.11e-01 2.05e+01 ... (remaining 9700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.20: 3618 29.20 - 58.39: 129 58.39 - 87.59: 15 87.59 - 116.78: 3 116.78 - 145.98: 3 Dihedral angle restraints: 3768 sinusoidal: 1686 harmonic: 2082 Sorted by residual: dihedral pdb=" C32 PEE A 312 " pdb=" C30 PEE A 312 " pdb=" C31 PEE A 312 " pdb=" O3 PEE A 312 " ideal model delta sinusoidal sigma weight residual 161.16 -52.86 -145.98 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C32 PEE C 312 " pdb=" C30 PEE C 312 " pdb=" C31 PEE C 312 " pdb=" O3 PEE C 312 " ideal model delta sinusoidal sigma weight residual 161.16 -52.87 -145.97 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C32 PEE B 312 " pdb=" C30 PEE B 312 " pdb=" C31 PEE B 312 " pdb=" O3 PEE B 312 " ideal model delta sinusoidal sigma weight residual 161.16 -52.89 -145.95 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 3765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 892 0.078 - 0.157: 74 0.157 - 0.235: 3 0.235 - 0.313: 54 0.313 - 0.391: 33 Chirality restraints: 1056 Sorted by residual: chirality pdb=" C2 PEE A 312 " pdb=" C1 PEE A 312 " pdb=" C3 PEE A 312 " pdb=" O2 PEE A 312 " both_signs ideal model delta sigma weight residual False -2.33 -2.72 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" C2 PEE C 312 " pdb=" C1 PEE C 312 " pdb=" C3 PEE C 312 " pdb=" O2 PEE C 312 " both_signs ideal model delta sigma weight residual False -2.33 -2.72 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" C17 CLR A 305 " pdb=" C13 CLR A 305 " pdb=" C16 CLR A 305 " pdb=" C20 CLR A 305 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 1053 not shown) Planarity restraints: 1035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 94 " 0.015 5.00e-02 4.00e+02 2.27e-02 8.24e-01 pdb=" N PRO A 95 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 94 " 0.015 5.00e-02 4.00e+02 2.26e-02 8.18e-01 pdb=" N PRO C 95 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 94 " 0.015 5.00e-02 4.00e+02 2.25e-02 8.12e-01 pdb=" N PRO B 95 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " 0.013 5.00e-02 4.00e+02 ... (remaining 1032 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 39 2.48 - 3.09: 4814 3.09 - 3.69: 9987 3.69 - 4.30: 16770 4.30 - 4.90: 27808 Nonbonded interactions: 59418 Sorted by model distance: nonbonded pdb=" OH TYR B 62 " pdb=" OE1 GLN C 175 " model vdw 1.878 3.040 nonbonded pdb=" OH TYR A 62 " pdb=" OE1 GLN B 175 " model vdw 1.878 3.040 nonbonded pdb=" OE1 GLN A 175 " pdb=" OH TYR C 62 " model vdw 1.878 3.040 nonbonded pdb=" O ALA A 132 " pdb=" OG1 THR A 136 " model vdw 2.243 3.040 nonbonded pdb=" O ALA B 132 " pdb=" OG1 THR B 136 " model vdw 2.243 3.040 ... (remaining 59413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.300 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 : 0.009 0.133 7089 Z= 0.458 Angle : 1.113 13.589 9705 Z= 0.394 Chirality : 0.100 0.391 1056 Planarity : 0.003 0.023 1035 Dihedral : 15.660 145.981 2442 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.33), residues: 714 helix: 1.73 (0.24), residues: 504 sheet: None (None), residues: 0 loop : -1.58 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 176 TYR 0.006 0.001 TYR C 177 PHE 0.005 0.001 PHE B 221 TRP 0.005 0.001 TRP C 190 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00920 / 0.46 ( 7086) covalent geometry : angle 1.11301 / 0.39 ( 9705) hydrogen bonds : bond 0.21610 / 14.76 ( 408) hydrogen bonds : angle 7.85021 / 5.55 ( 1224) Misc. bond : bond 0.00129 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 116 ASP cc_start: 0.8221 (t0) cc_final: 0.7866 (t0) REVERT: A 186 LYS cc_start: 0.7719 (mptt) cc_final: 0.7415 (ttmm) REVERT: B 144 PHE cc_start: 0.7667 (t80) cc_final: 0.7043 (t80) REVERT: B 186 LYS cc_start: 0.7894 (mptt) cc_final: 0.7558 (ttmm) REVERT: C 144 PHE cc_start: 0.7331 (t80) cc_final: 0.7103 (t80) REVERT: C 186 LYS cc_start: 0.7595 (mptt) cc_final: 0.7142 (ttmm) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.5154 time to fit residues: 41.2281 Evaluate side-chains 68 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.153813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.126723 restraints weight = 6890.502| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.41 r_work: 0.3235 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7089 Z= 0.156 Angle : 0.563 4.987 9705 Z= 0.269 Chirality : 0.039 0.137 1056 Planarity : 0.005 0.041 1035 Dihedral : 17.385 178.423 1209 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.31 % Allowed : 4.74 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.32), residues: 714 helix: 2.08 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.77 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 244 TYR 0.014 0.001 TYR B 154 PHE 0.015 0.001 PHE A 144 TRP 0.007 0.001 TRP A 190 HIS 0.004 0.001 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 7086) covalent geometry : angle 0.56348 / 0.27 ( 9705) hydrogen bonds : bond 0.05235 / 3.56 ( 408) hydrogen bonds : angle 4.89788 / 3.42 ( 1224) Misc. bond : bond 0.00098 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.170 Fit side-chains REVERT: A 116 ASP cc_start: 0.8482 (t0) cc_final: 0.8266 (t0) REVERT: A 186 LYS cc_start: 0.7922 (mptt) cc_final: 0.7709 (ttmm) REVERT: B 144 PHE cc_start: 0.7866 (t80) cc_final: 0.7386 (t80) REVERT: B 186 LYS cc_start: 0.8113 (mptt) cc_final: 0.7857 (ttmm) REVERT: C 170 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8212 (tp) REVERT: C 186 LYS cc_start: 0.7840 (mptt) cc_final: 0.7535 (ttmm) REVERT: C 240 MET cc_start: 0.8627 (mmp) cc_final: 0.8410 (tpt) outliers start: 8 outliers final: 1 residues processed: 71 average time/residue: 0.4562 time to fit residues: 34.1615 Evaluate side-chains 66 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain C residue 170 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 55 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 38 optimal weight: 0.0870 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 54 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.155629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.128785 restraints weight = 6773.756| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.40 r_work: 0.3284 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7089 Z= 0.122 Angle : 0.489 4.907 9705 Z= 0.232 Chirality : 0.036 0.120 1056 Planarity : 0.005 0.045 1035 Dihedral : 16.469 172.735 1209 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.98 % Allowed : 7.03 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.31), residues: 714 helix: 2.23 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.88 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 244 TYR 0.010 0.001 TYR A 177 PHE 0.014 0.001 PHE A 144 TRP 0.008 0.001 TRP C 102 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 7086) covalent geometry : angle 0.48873 / 0.23 ( 9705) hydrogen bonds : bond 0.04313 / 2.93 ( 408) hydrogen bonds : angle 4.55366 / 3.17 ( 1224) Misc. bond : bond 0.00087 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.143 Fit side-chains REVERT: A 106 TYR cc_start: 0.8868 (m-10) cc_final: 0.8545 (m-80) REVERT: A 144 PHE cc_start: 0.7605 (t80) cc_final: 0.6890 (t80) REVERT: A 176 ARG cc_start: 0.7418 (mtp85) cc_final: 0.7180 (ttt90) REVERT: A 186 LYS cc_start: 0.7824 (mptt) cc_final: 0.7572 (ttmm) REVERT: B 144 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7298 (t80) REVERT: B 175 GLN cc_start: 0.7461 (tt0) cc_final: 0.7234 (tt0) REVERT: B 186 LYS cc_start: 0.8099 (mptt) cc_final: 0.7803 (ttmm) REVERT: C 186 LYS cc_start: 0.7920 (mptt) cc_final: 0.7549 (ttmm) outliers start: 6 outliers final: 2 residues processed: 86 average time/residue: 0.4700 time to fit residues: 42.5009 Evaluate side-chains 78 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 144 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 19 optimal weight: 0.0870 chunk 50 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 67 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.154013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127113 restraints weight = 6881.223| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.41 r_work: 0.3265 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7089 Z= 0.132 Angle : 0.500 4.936 9705 Z= 0.237 Chirality : 0.037 0.120 1056 Planarity : 0.005 0.046 1035 Dihedral : 15.972 160.047 1209 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.31 % Allowed : 9.80 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.31), residues: 714 helix: 2.25 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.90 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 244 TYR 0.012 0.001 TYR C 177 PHE 0.013 0.001 PHE A 144 TRP 0.007 0.001 TRP C 161 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 7086) covalent geometry : angle 0.49990 / 0.24 ( 9705) hydrogen bonds : bond 0.04147 / 2.81 ( 408) hydrogen bonds : angle 4.44887 / 3.11 ( 1224) Misc. bond : bond 0.00089 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.220 Fit side-chains REVERT: A 106 TYR cc_start: 0.8871 (m-10) cc_final: 0.8588 (m-80) REVERT: A 144 PHE cc_start: 0.7710 (t80) cc_final: 0.6973 (t80) REVERT: A 186 LYS cc_start: 0.7937 (mptt) cc_final: 0.7670 (ttmm) REVERT: B 144 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7218 (t80) REVERT: B 175 GLN cc_start: 0.7484 (tt0) cc_final: 0.7234 (tt0) REVERT: B 176 ARG cc_start: 0.7387 (mtp85) cc_final: 0.7181 (ttt90) REVERT: B 186 LYS cc_start: 0.8124 (mptt) cc_final: 0.7816 (ttmm) REVERT: C 170 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8167 (tp) REVERT: C 186 LYS cc_start: 0.7936 (mptt) cc_final: 0.7680 (ttmm) outliers start: 8 outliers final: 3 residues processed: 85 average time/residue: 0.4960 time to fit residues: 44.6578 Evaluate side-chains 82 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 170 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 33 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 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 = 0.3786 r_free = 0.3786 target = 0.153754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.126691 restraints weight = 6877.362| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.42 r_work: 0.3261 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7089 Z= 0.134 Angle : 0.500 4.915 9705 Z= 0.235 Chirality : 0.037 0.122 1056 Planarity : 0.004 0.045 1035 Dihedral : 15.470 142.044 1209 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.63 % Allowed : 10.46 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.31), residues: 714 helix: 2.27 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.88 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 244 TYR 0.012 0.001 TYR C 177 PHE 0.011 0.001 PHE A 144 TRP 0.007 0.001 TRP C 161 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 7086) covalent geometry : angle 0.49958 / 0.23 ( 9705) hydrogen bonds : bond 0.04034 / 2.74 ( 408) hydrogen bonds : angle 4.40749 / 3.08 ( 1224) Misc. bond : bond 0.00097 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.6957 (t0) REVERT: A 106 TYR cc_start: 0.8866 (m-10) cc_final: 0.8533 (m-80) REVERT: A 144 PHE cc_start: 0.7706 (t80) cc_final: 0.7160 (t80) REVERT: A 186 LYS cc_start: 0.7958 (mptt) cc_final: 0.7713 (ttmm) REVERT: B 144 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7282 (t80) REVERT: B 175 GLN cc_start: 0.7489 (tt0) cc_final: 0.7277 (tt0) REVERT: B 186 LYS cc_start: 0.8071 (mptt) cc_final: 0.7766 (ttmm) REVERT: C 21 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6735 (t70) REVERT: C 170 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8086 (tp) REVERT: C 186 LYS cc_start: 0.7935 (mptt) cc_final: 0.7664 (ttmm) outliers start: 10 outliers final: 2 residues processed: 88 average time/residue: 0.4970 time to fit residues: 46.0496 Evaluate side-chains 84 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 170 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 3 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 42 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.151181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124128 restraints weight = 6924.530| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.41 r_work: 0.3222 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7089 Z= 0.178 Angle : 0.556 5.022 9705 Z= 0.261 Chirality : 0.039 0.120 1056 Planarity : 0.005 0.036 1035 Dihedral : 15.391 137.015 1209 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.80 % Allowed : 10.78 % Favored : 87.42 % 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: 1.60 (0.31), residues: 714 helix: 2.08 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.96 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 244 TYR 0.017 0.002 TYR C 177 PHE 0.020 0.001 PHE C 144 TRP 0.007 0.001 TRP A 190 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 ( 7086) covalent geometry : angle 0.55625 / 0.26 ( 9705) hydrogen bonds : bond 0.04415 / 3.02 ( 408) hydrogen bonds : angle 4.51442 / 3.16 ( 1224) Misc. bond : bond 0.00132 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.227 Fit side-chains REVERT: A 175 GLN cc_start: 0.7420 (tt0) cc_final: 0.6611 (mp10) REVERT: A 186 LYS cc_start: 0.7956 (mptt) cc_final: 0.7716 (ttmm) REVERT: B 144 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7309 (t80) REVERT: B 175 GLN cc_start: 0.7462 (tt0) cc_final: 0.6769 (mp10) REVERT: B 186 LYS cc_start: 0.8152 (mptt) cc_final: 0.7854 (ttmm) REVERT: C 21 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.6709 (t0) REVERT: C 170 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8197 (tp) REVERT: C 186 LYS cc_start: 0.7993 (mptt) cc_final: 0.7654 (ttmm) outliers start: 11 outliers final: 2 residues processed: 80 average time/residue: 0.5522 time to fit residues: 46.4313 Evaluate side-chains 80 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 170 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 69 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 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 = 0.3779 r_free = 0.3779 target = 0.153170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127098 restraints weight = 6787.625| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.34 r_work: 0.3272 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7089 Z= 0.136 Angle : 0.509 4.963 9705 Z= 0.240 Chirality : 0.037 0.121 1056 Planarity : 0.004 0.036 1035 Dihedral : 14.957 129.474 1209 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.63 % Allowed : 10.78 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.31), residues: 714 helix: 2.22 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.96 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.011 0.001 TYR C 177 PHE 0.021 0.001 PHE A 144 TRP 0.007 0.001 TRP C 190 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 7086) covalent geometry : angle 0.50928 / 0.24 ( 9705) hydrogen bonds : bond 0.04044 / 2.75 ( 408) hydrogen bonds : angle 4.41123 / 3.08 ( 1224) Misc. bond : bond 0.00095 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.6843 (t0) REVERT: B 144 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7195 (t80) REVERT: B 175 GLN cc_start: 0.7469 (tt0) cc_final: 0.6832 (mp10) REVERT: B 186 LYS cc_start: 0.8066 (mptt) cc_final: 0.7797 (ttmm) REVERT: C 21 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.6765 (t70) REVERT: C 170 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8092 (tp) REVERT: C 186 LYS cc_start: 0.7922 (mptt) cc_final: 0.7664 (ttmm) outliers start: 10 outliers final: 3 residues processed: 85 average time/residue: 0.5138 time to fit residues: 45.9655 Evaluate side-chains 85 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 170 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.153379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127193 restraints weight = 6875.458| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.35 r_work: 0.3300 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7089 Z= 0.134 Angle : 0.513 4.947 9705 Z= 0.242 Chirality : 0.037 0.121 1056 Planarity : 0.004 0.036 1035 Dihedral : 14.693 123.044 1209 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.80 % Allowed : 10.78 % Favored : 87.42 % 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: 1.79 (0.31), residues: 714 helix: 2.24 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.94 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.010 0.001 TYR C 155 PHE 0.024 0.001 PHE A 144 TRP 0.007 0.001 TRP A 190 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 7086) covalent geometry : angle 0.51329 / 0.24 ( 9705) hydrogen bonds : bond 0.03986 / 2.72 ( 408) hydrogen bonds : angle 4.39414 / 3.07 ( 1224) Misc. bond : bond 0.00097 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.6922 (t0) REVERT: B 144 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.7198 (t80) REVERT: B 175 GLN cc_start: 0.7389 (tt0) cc_final: 0.6758 (mp10) REVERT: B 186 LYS cc_start: 0.8072 (mptt) cc_final: 0.7792 (ttmm) REVERT: C 21 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6610 (t0) REVERT: C 170 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8162 (tp) REVERT: C 176 ARG cc_start: 0.7441 (tpt90) cc_final: 0.7139 (mtp180) REVERT: C 178 GLN cc_start: 0.8109 (mt0) cc_final: 0.7693 (mp10) REVERT: C 186 LYS cc_start: 0.7883 (mptt) cc_final: 0.7608 (ttmm) outliers start: 11 outliers final: 3 residues processed: 86 average time/residue: 0.5249 time to fit residues: 47.5247 Evaluate side-chains 85 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 170 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 55 optimal weight: 0.0270 chunk 18 optimal weight: 0.6980 overall best weight: 0.6840 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.153394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127123 restraints weight = 6861.971| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.35 r_work: 0.3300 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7089 Z= 0.137 Angle : 0.513 5.039 9705 Z= 0.242 Chirality : 0.037 0.121 1056 Planarity : 0.004 0.037 1035 Dihedral : 14.519 117.852 1209 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.47 % Allowed : 11.11 % Favored : 87.42 % 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: 1.80 (0.31), residues: 714 helix: 2.24 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.92 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.009 0.001 TYR C 155 PHE 0.022 0.001 PHE A 144 TRP 0.006 0.001 TRP A 190 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 7086) covalent geometry : angle 0.51330 / 0.24 ( 9705) hydrogen bonds : bond 0.03990 / 2.73 ( 408) hydrogen bonds : angle 4.38747 / 3.07 ( 1224) Misc. bond : bond 0.00099 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.6917 (t0) REVERT: B 144 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7240 (t80) REVERT: B 175 GLN cc_start: 0.7373 (tt0) cc_final: 0.6764 (mp10) REVERT: B 186 LYS cc_start: 0.8066 (mptt) cc_final: 0.7782 (ttmm) REVERT: C 21 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.6600 (t0) REVERT: C 170 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8160 (tp) REVERT: C 178 GLN cc_start: 0.8195 (mt0) cc_final: 0.7755 (mp10) REVERT: C 186 LYS cc_start: 0.7880 (mptt) cc_final: 0.7597 (ttmm) outliers start: 9 outliers final: 3 residues processed: 80 average time/residue: 0.5213 time to fit residues: 43.6881 Evaluate side-chains 82 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 170 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 58 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.153563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127337 restraints weight = 6811.751| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.35 r_work: 0.3298 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7089 Z= 0.136 Angle : 0.513 5.020 9705 Z= 0.242 Chirality : 0.037 0.121 1056 Planarity : 0.004 0.036 1035 Dihedral : 14.371 113.348 1209 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.47 % Allowed : 11.27 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.31), residues: 714 helix: 2.25 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.93 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.009 0.001 TYR C 155 PHE 0.029 0.001 PHE A 144 TRP 0.007 0.001 TRP A 190 HIS 0.002 0.000 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 7086) covalent geometry : angle 0.51303 / 0.24 ( 9705) hydrogen bonds : bond 0.03979 / 2.72 ( 408) hydrogen bonds : angle 4.39339 / 3.07 ( 1224) Misc. bond : bond 0.00098 / 0.04 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.6912 (t0) REVERT: B 144 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.7238 (t80) REVERT: B 175 GLN cc_start: 0.7368 (tt0) cc_final: 0.6783 (mp10) REVERT: B 186 LYS cc_start: 0.8062 (mptt) cc_final: 0.7778 (ttmm) REVERT: C 21 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.6610 (t0) REVERT: C 170 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8164 (tp) REVERT: C 178 GLN cc_start: 0.8203 (mt0) cc_final: 0.7756 (mp10) REVERT: C 186 LYS cc_start: 0.7878 (mptt) cc_final: 0.7591 (ttmm) outliers start: 9 outliers final: 3 residues processed: 80 average time/residue: 0.4839 time to fit residues: 40.7885 Evaluate side-chains 82 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 170 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 58 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.153755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.127543 restraints weight = 6802.858| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.35 r_work: 0.3305 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7089 Z= 0.133 Angle : 0.508 4.973 9705 Z= 0.240 Chirality : 0.037 0.121 1056 Planarity : 0.004 0.036 1035 Dihedral : 14.243 109.030 1209 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.31 % Allowed : 11.27 % Favored : 87.42 % 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: 1.84 (0.31), residues: 714 helix: 2.27 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.91 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.008 0.001 TYR B 154 PHE 0.026 0.001 PHE A 144 TRP 0.007 0.001 TRP A 190 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 7086) covalent geometry : angle 0.50831 / 0.24 ( 9705) hydrogen bonds : bond 0.03946 / 2.70 ( 408) hydrogen bonds : angle 4.38241 / 3.06 ( 1224) Misc. bond : bond 0.00092 / 0.04 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1671.75 seconds wall clock time: 29 minutes 17.04 seconds (1757.04 seconds total)