Starting phenix.real_space_refine on Fri Aug 22 14:03:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fh5_50440/08_2025/9fh5_50440.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fh5_50440/08_2025/9fh5_50440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fh5_50440/08_2025/9fh5_50440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fh5_50440/08_2025/9fh5_50440.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fh5_50440/08_2025/9fh5_50440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fh5_50440/08_2025/9fh5_50440.map" } resolution = 3.8 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= 0.344 sd= 1.454 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 1160 2.51 5 N 280 2.21 5 O 280 1.98 5 H 2040 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3780 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "B" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "C" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "D" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "F" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "G" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "H" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "I" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "J" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "K" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "L" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "M" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "N" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "O" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "P" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "Q" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "R" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "S" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "T" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 189 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Time building chain proxies: 0.72, per 1000 atoms: 0.19 Number of scatterers: 3780 At special positions: 0 Unit cell: (66.096, 57.936, 40.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 O 280 8.00 N 280 7.00 C 1160 6.00 H 2040 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.21 Conformation dependent library (CDL) restraints added in 63.3 milliseconds Enol-peptide restraints added in 0.0 nanoseconds 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 400 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.307A pdb=" N ILE A 31 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE E 31 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE I 31 " --> pdb=" O ILE M 32 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE M 31 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 removed outlier: 6.506A pdb=" N VAL A 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL E 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL I 39 " --> pdb=" O VAL M 40 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL M 39 " --> pdb=" O VAL Q 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 31 through 33 removed outlier: 6.556A pdb=" N ILE B 31 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE F 31 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE J 31 " --> pdb=" O ILE N 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 39 through 40 removed outlier: 6.642A pdb=" N VAL B 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL F 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL J 39 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL N 39 " --> pdb=" O VAL R 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 31 through 33 removed outlier: 6.519A pdb=" N ILE C 31 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE G 31 " --> pdb=" O ILE K 32 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE K 31 " --> pdb=" O ILE O 32 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE O 31 " --> pdb=" O ILE S 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.729A pdb=" N VAL C 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL G 39 " --> pdb=" O VAL K 40 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL K 39 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL O 39 " --> pdb=" O VAL S 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 31 through 33 removed outlier: 3.543A pdb=" N ILE L 32 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE P 32 " --> pdb=" O ILE L 31 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 39 through 40 removed outlier: 6.445A pdb=" N VAL D 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL H 39 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL L 39 " --> pdb=" O VAL P 40 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL P 39 " --> pdb=" O VAL T 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 8 hydrogen bonds defined for protein. 24 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: 0.61 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 2040 1.17 - 1.33: 454 1.33 - 1.49: 366 1.49 - 1.65: 860 1.65 - 1.81: 40 Bond restraints: 3760 Sorted by residual: bond pdb=" N GLY Q 37 " pdb=" H GLY Q 37 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N MET E 35 " pdb=" H MET E 35 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ILE J 32 " pdb=" H ILE J 32 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLY J 37 " pdb=" H GLY J 37 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ILE R 41 " pdb=" H ILE R 41 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 3755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 4820 1.69 - 3.38: 1353 3.38 - 5.06: 393 5.06 - 6.75: 295 6.75 - 8.44: 39 Bond angle restraints: 6900 Sorted by residual: angle pdb=" C LEU G 34 " pdb=" CA LEU G 34 " pdb=" CB LEU G 34 " ideal model delta sigma weight residual 111.73 118.96 -7.23 1.42e+00 4.96e-01 2.59e+01 angle pdb=" C LEU S 34 " pdb=" CA LEU S 34 " pdb=" CB LEU S 34 " ideal model delta sigma weight residual 111.51 119.38 -7.87 1.58e+00 4.01e-01 2.48e+01 angle pdb=" C LEU O 34 " pdb=" CA LEU O 34 " pdb=" CB LEU O 34 " ideal model delta sigma weight residual 111.51 119.02 -7.51 1.58e+00 4.01e-01 2.26e+01 angle pdb=" C LEU K 34 " pdb=" CA LEU K 34 " pdb=" CB LEU K 34 " ideal model delta sigma weight residual 111.51 118.91 -7.40 1.58e+00 4.01e-01 2.19e+01 angle pdb=" C LEU Q 34 " pdb=" CA LEU Q 34 " pdb=" CB LEU Q 34 " ideal model delta sigma weight residual 111.73 118.34 -6.61 1.42e+00 4.96e-01 2.17e+01 ... (remaining 6895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.52: 1390 14.52 - 29.03: 92 29.03 - 43.55: 20 43.55 - 58.07: 98 58.07 - 72.59: 40 Dihedral angle restraints: 1640 sinusoidal: 980 harmonic: 660 Sorted by residual: dihedral pdb=" CA GLY J 37 " pdb=" C GLY J 37 " pdb=" N GLY J 38 " pdb=" CA GLY J 38 " ideal model delta harmonic sigma weight residual -180.00 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" C LEU G 34 " pdb=" N LEU G 34 " pdb=" CA LEU G 34 " pdb=" CB LEU G 34 " ideal model delta harmonic sigma weight residual -122.60 -133.60 11.00 0 2.50e+00 1.60e-01 1.94e+01 dihedral pdb=" C LEU K 34 " pdb=" N LEU K 34 " pdb=" CA LEU K 34 " pdb=" CB LEU K 34 " ideal model delta harmonic sigma weight residual -122.60 -133.38 10.78 0 2.50e+00 1.60e-01 1.86e+01 ... (remaining 1637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 155 0.066 - 0.132: 105 0.132 - 0.198: 57 0.198 - 0.264: 13 0.264 - 0.330: 10 Chirality restraints: 340 Sorted by residual: chirality pdb=" CA LEU G 34 " pdb=" N LEU G 34 " pdb=" C LEU G 34 " pdb=" CB LEU G 34 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA LEU K 34 " pdb=" N LEU K 34 " pdb=" C LEU K 34 " pdb=" CB LEU K 34 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA LEU O 34 " pdb=" N LEU O 34 " pdb=" C LEU O 34 " pdb=" CB LEU O 34 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 337 not shown) Planarity restraints: 520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 37 " 0.028 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" N GLY D 38 " -0.087 2.00e-02 2.50e+03 pdb=" CA GLY D 38 " 0.025 2.00e-02 2.50e+03 pdb=" H GLY D 38 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY H 37 " 0.027 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" N GLY H 38 " -0.085 2.00e-02 2.50e+03 pdb=" CA GLY H 38 " 0.024 2.00e-02 2.50e+03 pdb=" H GLY H 38 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY J 37 " 0.026 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" N GLY J 38 " -0.085 2.00e-02 2.50e+03 pdb=" CA GLY J 38 " 0.024 2.00e-02 2.50e+03 pdb=" H GLY J 38 " 0.034 2.00e-02 2.50e+03 ... (remaining 517 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.38: 1158 2.38 - 2.94: 8789 2.94 - 3.49: 10572 3.49 - 4.05: 13425 4.05 - 4.60: 19822 Nonbonded interactions: 53766 Sorted by model distance: nonbonded pdb=" HB VAL J 36 " pdb=" H GLY N 37 " model vdw 1.831 2.270 nonbonded pdb=" HB VAL F 36 " pdb=" H GLY J 37 " model vdw 1.833 2.270 nonbonded pdb=" O VAL H 39 " pdb=" H VAL L 40 " model vdw 1.843 2.450 nonbonded pdb=" HB VAL A 36 " pdb=" H GLY E 37 " model vdw 1.846 2.270 nonbonded pdb=" O VAL L 39 " pdb=" H VAL P 40 " model vdw 1.848 2.450 ... (remaining 53761 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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 group one per residue 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: 1.230 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: 0.030 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.510 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.010 0.028 1720 Z= 0.658 Angle : 1.973 7.873 2300 Z= 1.260 Chirality : 0.113 0.330 340 Planarity : 0.010 0.026 260 Dihedral : 9.177 23.364 540 Min Nonbonded Distance : 2.680 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 5.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.53), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.33 (0.40), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.01022 ( 1720) covalent geometry : angle 1.97304 ( 2300) hydrogen bonds : bond 0.20338 ( 8) hydrogen bonds : angle 14.46951 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 41 ILE cc_start: 0.8946 (mm) cc_final: 0.8599 (pt) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0513 time to fit residues: 4.5204 Evaluate side-chains 48 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.146712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.119982 restraints weight = 10013.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.126037 restraints weight = 5080.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.130599 restraints weight = 3087.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.134058 restraints weight = 2067.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.136489 restraints weight = 1470.691| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 1720 Z= 0.252 Angle : 0.883 6.041 2300 Z= 0.436 Chirality : 0.067 0.147 340 Planarity : 0.003 0.007 260 Dihedral : 8.455 18.425 260 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.62 % Allowed : 17.50 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.54), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.48 (0.41), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 1720) covalent geometry : angle 0.88279 ( 2300) hydrogen bonds : bond 0.05862 ( 8) hydrogen bonds : angle 9.71141 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.072 Fit side-chains REVERT: G 32 ILE cc_start: 0.9069 (mt) cc_final: 0.8759 (mp) outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.0570 time to fit residues: 3.6802 Evaluate side-chains 45 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.148797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.121727 restraints weight = 9755.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.127866 restraints weight = 5107.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.132467 restraints weight = 3121.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.136026 restraints weight = 2098.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.138583 restraints weight = 1496.223| |-----------------------------------------------------------------------------| r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1720 Z= 0.158 Angle : 0.779 5.879 2300 Z= 0.374 Chirality : 0.065 0.145 340 Planarity : 0.002 0.006 260 Dihedral : 6.910 15.349 260 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.25 % Allowed : 21.88 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.56), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.14 (0.43), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 1720) covalent geometry : angle 0.77912 ( 2300) hydrogen bonds : bond 0.03794 ( 8) hydrogen bonds : angle 9.13991 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.090 Fit side-chains REVERT: G 32 ILE cc_start: 0.9122 (mt) cc_final: 0.8723 (mp) REVERT: N 32 ILE cc_start: 0.8645 (mt) cc_final: 0.8305 (mp) REVERT: S 40 VAL cc_start: 0.7761 (OUTLIER) cc_final: 0.7498 (m) outliers start: 2 outliers final: 1 residues processed: 48 average time/residue: 0.0525 time to fit residues: 3.3603 Evaluate side-chains 48 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain S residue 40 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.151658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.123388 restraints weight = 9710.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.129772 restraints weight = 4996.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.134589 restraints weight = 3022.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.138256 restraints weight = 2017.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.140975 restraints weight = 1447.238| |-----------------------------------------------------------------------------| r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1720 Z= 0.131 Angle : 0.718 5.160 2300 Z= 0.345 Chirality : 0.066 0.145 340 Planarity : 0.002 0.005 260 Dihedral : 6.323 14.939 260 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.62 % Allowed : 25.00 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.56), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.12 (0.42), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 1720) covalent geometry : angle 0.71847 ( 2300) hydrogen bonds : bond 0.02969 ( 8) hydrogen bonds : angle 8.72860 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.082 Fit side-chains REVERT: O 32 ILE cc_start: 0.8995 (mt) cc_final: 0.8699 (mp) outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.0554 time to fit residues: 3.4600 Evaluate side-chains 44 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 34 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.0270 chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.158946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.129480 restraints weight = 9359.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.136501 restraints weight = 4744.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.141658 restraints weight = 2841.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.145540 restraints weight = 1865.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.148195 restraints weight = 1301.427| |-----------------------------------------------------------------------------| r_work (final): 0.4431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1720 Z= 0.119 Angle : 0.681 5.510 2300 Z= 0.328 Chirality : 0.066 0.139 340 Planarity : 0.002 0.007 260 Dihedral : 5.984 14.509 260 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.25 % Allowed : 24.38 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.56), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.25 (0.43), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 1720) covalent geometry : angle 0.68127 ( 2300) hydrogen bonds : bond 0.02994 ( 8) hydrogen bonds : angle 8.45969 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.099 Fit side-chains REVERT: G 32 ILE cc_start: 0.9148 (mt) cc_final: 0.8756 (mp) REVERT: L 35 MET cc_start: 0.7752 (ttm) cc_final: 0.7528 (ttp) REVERT: N 32 ILE cc_start: 0.8722 (mt) cc_final: 0.8419 (mp) REVERT: O 32 ILE cc_start: 0.8970 (mt) cc_final: 0.8682 (mp) outliers start: 2 outliers final: 1 residues processed: 50 average time/residue: 0.0541 time to fit residues: 3.6167 Evaluate side-chains 46 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 34 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.174329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.139786 restraints weight = 9963.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.147545 restraints weight = 4837.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.152754 restraints weight = 2813.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.156394 restraints weight = 1840.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.159036 restraints weight = 1291.979| |-----------------------------------------------------------------------------| r_work (final): 0.4401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1720 Z= 0.173 Angle : 0.705 5.759 2300 Z= 0.349 Chirality : 0.064 0.141 340 Planarity : 0.002 0.006 260 Dihedral : 6.199 15.203 260 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.88 % Allowed : 27.50 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.53), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.71 (0.41), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 1720) covalent geometry : angle 0.70544 ( 2300) hydrogen bonds : bond 0.02995 ( 8) hydrogen bonds : angle 9.10302 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.072 Fit side-chains REVERT: G 32 ILE cc_start: 0.9156 (mt) cc_final: 0.8755 (mp) REVERT: O 32 ILE cc_start: 0.8948 (mt) cc_final: 0.8683 (mp) REVERT: S 40 VAL cc_start: 0.7995 (OUTLIER) cc_final: 0.7752 (m) outliers start: 3 outliers final: 2 residues processed: 45 average time/residue: 0.0435 time to fit residues: 2.6632 Evaluate side-chains 45 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain S residue 40 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.155951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.126661 restraints weight = 9502.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.133381 restraints weight = 4924.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.138237 restraints weight = 2973.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.141908 restraints weight = 1985.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.144648 restraints weight = 1412.728| |-----------------------------------------------------------------------------| r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1720 Z= 0.141 Angle : 0.686 6.403 2300 Z= 0.336 Chirality : 0.065 0.137 340 Planarity : 0.002 0.007 260 Dihedral : 5.979 15.444 260 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.88 % Allowed : 27.50 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.53), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.84 (0.41), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 1720) covalent geometry : angle 0.68568 ( 2300) hydrogen bonds : bond 0.03100 ( 8) hydrogen bonds : angle 8.85911 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.058 Fit side-chains REVERT: G 32 ILE cc_start: 0.9195 (mt) cc_final: 0.8772 (mp) REVERT: O 32 ILE cc_start: 0.8916 (mt) cc_final: 0.8662 (mp) REVERT: S 40 VAL cc_start: 0.8001 (OUTLIER) cc_final: 0.7762 (m) outliers start: 3 outliers final: 1 residues processed: 46 average time/residue: 0.0484 time to fit residues: 2.9320 Evaluate side-chains 44 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain S residue 40 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 8.9990 chunk 17 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 16 optimal weight: 0.0980 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.156288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.129368 restraints weight = 9834.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.136058 restraints weight = 4828.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.141170 restraints weight = 2825.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.144564 restraints weight = 1811.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.147110 restraints weight = 1256.837| |-----------------------------------------------------------------------------| r_work (final): 0.4539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1720 Z= 0.101 Angle : 0.676 5.913 2300 Z= 0.318 Chirality : 0.067 0.139 340 Planarity : 0.001 0.006 260 Dihedral : 5.438 16.045 260 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 5.00 % Allowed : 23.75 % Favored : 71.25 % 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 aren not related in a simple way. whole: -0.93 (0.54), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.70 (0.41), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 1720) covalent geometry : angle 0.67589 ( 2300) hydrogen bonds : bond 0.03373 ( 8) hydrogen bonds : angle 8.23670 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.106 Fit side-chains REVERT: G 32 ILE cc_start: 0.9133 (mt) cc_final: 0.8744 (mp) REVERT: J 32 ILE cc_start: 0.8884 (mt) cc_final: 0.8657 (mp) REVERT: M 34 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7370 (tt) REVERT: N 32 ILE cc_start: 0.8636 (mt) cc_final: 0.8376 (mp) REVERT: O 32 ILE cc_start: 0.8875 (mt) cc_final: 0.8549 (mp) REVERT: Q 34 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7650 (tt) REVERT: S 32 ILE cc_start: 0.8893 (mt) cc_final: 0.8538 (tp) REVERT: S 40 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7776 (m) outliers start: 8 outliers final: 1 residues processed: 52 average time/residue: 0.0595 time to fit residues: 4.1257 Evaluate side-chains 49 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain S residue 40 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 0.0470 chunk 9 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.165087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.136812 restraints weight = 9111.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.144213 restraints weight = 4448.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.149565 restraints weight = 2583.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.153213 restraints weight = 1639.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.155918 restraints weight = 1124.986| |-----------------------------------------------------------------------------| r_work (final): 0.4581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1720 Z= 0.095 Angle : 0.658 6.315 2300 Z= 0.309 Chirality : 0.067 0.146 340 Planarity : 0.001 0.006 260 Dihedral : 5.094 15.136 260 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.12 % Allowed : 24.38 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.54), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.71 (0.41), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 1720) covalent geometry : angle 0.65762 ( 2300) hydrogen bonds : bond 0.03474 ( 8) hydrogen bonds : angle 7.80421 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.092 Fit side-chains REVERT: G 32 ILE cc_start: 0.9143 (mt) cc_final: 0.8747 (mp) REVERT: J 32 ILE cc_start: 0.8866 (mt) cc_final: 0.8635 (mp) REVERT: N 32 ILE cc_start: 0.8607 (mt) cc_final: 0.8322 (mp) REVERT: O 32 ILE cc_start: 0.8882 (mt) cc_final: 0.8643 (mp) REVERT: Q 34 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7641 (tt) REVERT: S 40 VAL cc_start: 0.8032 (OUTLIER) cc_final: 0.7797 (m) outliers start: 5 outliers final: 2 residues processed: 50 average time/residue: 0.0604 time to fit residues: 4.0100 Evaluate side-chains 51 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain S residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 8.9990 chunk 3 optimal weight: 0.0570 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.186624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.152233 restraints weight = 9328.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.160845 restraints weight = 4427.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.166542 restraints weight = 2494.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.170219 restraints weight = 1558.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.172706 restraints weight = 1062.646| |-----------------------------------------------------------------------------| r_work (final): 0.4615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1720 Z= 0.098 Angle : 0.670 7.257 2300 Z= 0.309 Chirality : 0.066 0.143 340 Planarity : 0.001 0.013 260 Dihedral : 4.963 14.940 260 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 3.12 % Allowed : 24.38 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.55), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.42), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 1720) covalent geometry : angle 0.67049 ( 2300) hydrogen bonds : bond 0.03552 ( 8) hydrogen bonds : angle 7.55971 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.102 Fit side-chains REVERT: J 32 ILE cc_start: 0.8823 (mt) cc_final: 0.8602 (mp) REVERT: K 32 ILE cc_start: 0.8867 (mt) cc_final: 0.8536 (mp) REVERT: O 32 ILE cc_start: 0.8829 (mt) cc_final: 0.8596 (mp) REVERT: Q 32 ILE cc_start: 0.7328 (OUTLIER) cc_final: 0.6798 (mt) REVERT: Q 34 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7629 (tt) REVERT: S 32 ILE cc_start: 0.8736 (mt) cc_final: 0.8307 (mm) outliers start: 5 outliers final: 1 residues processed: 50 average time/residue: 0.0623 time to fit residues: 4.1562 Evaluate side-chains 48 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.233005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.147409 restraints weight = 10912.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.154561 restraints weight = 5436.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.159460 restraints weight = 3297.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.162961 restraints weight = 2252.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.165285 restraints weight = 1637.144| |-----------------------------------------------------------------------------| r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 1720 Z= 0.189 Angle : 0.708 6.665 2300 Z= 0.353 Chirality : 0.065 0.146 340 Planarity : 0.003 0.010 260 Dihedral : 5.844 14.890 260 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 25.62 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.53), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.41), residues: 240 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 1720) covalent geometry : angle 0.70830 ( 2300) hydrogen bonds : bond 0.02745 ( 8) hydrogen bonds : angle 8.58658 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1119.31 seconds wall clock time: 19 minutes 41.18 seconds (1181.18 seconds total)