Starting phenix.real_space_refine on Sat Apr 4 23:09:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u9h_63964/04_2026/9u9h_63964_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u9h_63964/04_2026/9u9h_63964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u9h_63964/04_2026/9u9h_63964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u9h_63964/04_2026/9u9h_63964.map" model { file = "/net/cci-nas-00/data/ceres_data/9u9h_63964/04_2026/9u9h_63964_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u9h_63964/04_2026/9u9h_63964_neut.cif" } resolution = 3.23 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= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 44 5.16 5 C 3836 2.51 5 N 773 2.21 5 O 924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5586 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 471 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "B" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 822 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "D" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 471 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 822 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "G" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 471 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "H" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 822 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "J" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 471 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 822 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'PX4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PX4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PX4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PX4': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'PX4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PX4': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PX4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.29, per 1000 atoms: 0.23 Number of scatterers: 5586 At special positions: 0 Unit cell: (76.26, 80.36, 132.02, 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 44 16.00 P 9 15.00 O 924 8.00 N 773 7.00 C 3836 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=0, symmetry=0 Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 288.8 milliseconds 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 85.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 12 through 36 removed outlier: 3.533A pdb=" N SER A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 67 removed outlier: 3.577A pdb=" N TRP A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 73 Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 92 through 107 removed outlier: 3.527A pdb=" N LEU B 96 " --> pdb=" O PRO B 92 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 135 Processing helix chain 'B' and resid 137 through 159 removed outlier: 3.693A pdb=" N ILE B 159 " --> pdb=" O TYR B 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 36 removed outlier: 3.577A pdb=" N VAL D 14 " --> pdb=" O TYR D 10 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS D 35 " --> pdb=" O ILE D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 67 Processing helix chain 'E' and resid 58 through 73 removed outlier: 4.049A pdb=" N THR E 62 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 63 " --> pdb=" O ASP E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 88 Processing helix chain 'E' and resid 92 through 107 removed outlier: 3.647A pdb=" N LEU E 96 " --> pdb=" O PRO E 92 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET E 106 " --> pdb=" O LEU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 135 Processing helix chain 'E' and resid 137 through 158 Processing helix chain 'G' and resid 11 through 34 removed outlier: 3.521A pdb=" N SER G 34 " --> pdb=" O PHE G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 67 removed outlier: 3.972A pdb=" N VAL G 45 " --> pdb=" O ARG G 41 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU G 46 " --> pdb=" O THR G 42 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER G 47 " --> pdb=" O TRP G 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 74 removed outlier: 3.580A pdb=" N TYR H 74 " --> pdb=" O VAL H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 88 Processing helix chain 'H' and resid 92 through 107 removed outlier: 3.722A pdb=" N LEU H 96 " --> pdb=" O PRO H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 135 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'J' and resid 11 through 36 removed outlier: 4.097A pdb=" N LEU J 15 " --> pdb=" O PHE J 11 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER J 34 " --> pdb=" O PHE J 30 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS J 35 " --> pdb=" O ILE J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 67 removed outlier: 3.543A pdb=" N VAL J 45 " --> pdb=" O ARG J 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 73 Processing helix chain 'K' and resid 76 through 88 Processing helix chain 'K' and resid 92 through 107 removed outlier: 3.678A pdb=" N LEU K 96 " --> pdb=" O PRO K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 135 Processing helix chain 'K' and resid 137 through 159 removed outlier: 3.599A pdb=" N ILE K 159 " --> pdb=" O TYR K 155 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1293 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: 0.86 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 751 1.32 - 1.45: 1486 1.45 - 1.57: 3354 1.57 - 1.69: 18 1.69 - 1.82: 76 Bond restraints: 5685 Sorted by residual: bond pdb=" O3 PX4 D 101 " pdb=" P1 PX4 D 101 " ideal model delta sigma weight residual 1.649 1.602 0.047 2.00e-02 2.50e+03 5.46e+00 bond pdb=" C1 PX4 E 201 " pdb=" O3 PX4 E 201 " ideal model delta sigma weight residual 1.409 1.453 -0.044 2.00e-02 2.50e+03 4.92e+00 bond pdb=" O3 PX4 E 201 " pdb=" P1 PX4 E 201 " ideal model delta sigma weight residual 1.649 1.605 0.044 2.00e-02 2.50e+03 4.89e+00 bond pdb=" O3 PX4 K 201 " pdb=" P1 PX4 K 201 " ideal model delta sigma weight residual 1.649 1.606 0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" C1 PX4 K 201 " pdb=" O3 PX4 K 201 " ideal model delta sigma weight residual 1.409 1.452 -0.043 2.00e-02 2.50e+03 4.67e+00 ... (remaining 5680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 7532 1.92 - 3.83: 103 3.83 - 5.75: 13 5.75 - 7.67: 6 7.67 - 9.58: 3 Bond angle restraints: 7657 Sorted by residual: angle pdb=" O3 PX4 E 201 " pdb=" P1 PX4 E 201 " pdb=" O4 PX4 E 201 " ideal model delta sigma weight residual 93.64 103.22 -9.58 3.00e+00 1.11e-01 1.02e+01 angle pdb=" O3 PX4 K 201 " pdb=" P1 PX4 K 201 " pdb=" O4 PX4 K 201 " ideal model delta sigma weight residual 93.64 102.54 -8.90 3.00e+00 1.11e-01 8.81e+00 angle pdb=" C GLY B 112 " pdb=" N ASN B 113 " pdb=" CA ASN B 113 " ideal model delta sigma weight residual 121.54 127.11 -5.57 1.91e+00 2.74e-01 8.49e+00 angle pdb=" N ASN B 58 " pdb=" CA ASN B 58 " pdb=" C ASN B 58 " ideal model delta sigma weight residual 110.61 106.98 3.63 1.25e+00 6.40e-01 8.43e+00 angle pdb=" CA ASN B 113 " pdb=" CB ASN B 113 " pdb=" CG ASN B 113 " ideal model delta sigma weight residual 112.60 115.39 -2.79 1.00e+00 1.00e+00 7.81e+00 ... (remaining 7652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.77: 3233 33.77 - 67.54: 166 67.54 - 101.31: 6 101.31 - 135.08: 1 135.08 - 168.85: 6 Dihedral angle restraints: 3412 sinusoidal: 1488 harmonic: 1924 Sorted by residual: dihedral pdb=" O5 PX4 A 101 " pdb=" C7 PX4 A 101 " pdb=" C8 PX4 A 101 " pdb=" O7 PX4 A 101 " ideal model delta sinusoidal sigma weight residual 59.95 -108.90 168.85 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" O5 PX4 G 101 " pdb=" C7 PX4 G 101 " pdb=" C8 PX4 G 101 " pdb=" O7 PX4 G 101 " ideal model delta sinusoidal sigma weight residual 59.95 -138.91 -161.14 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" O5 PX4 E 201 " pdb=" C7 PX4 E 201 " pdb=" C8 PX4 E 201 " pdb=" O7 PX4 E 201 " ideal model delta sinusoidal sigma weight residual 59.95 -139.62 -160.43 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 3409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 626 0.036 - 0.073: 251 0.073 - 0.109: 39 0.109 - 0.145: 8 0.145 - 0.182: 5 Chirality restraints: 929 Sorted by residual: chirality pdb=" CA ASN B 113 " pdb=" N ASN B 113 " pdb=" C ASN B 113 " pdb=" CB ASN B 113 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" C7 PX4 E 201 " pdb=" C6 PX4 E 201 " pdb=" C8 PX4 E 201 " pdb=" O7 PX4 E 201 " both_signs ideal model delta sigma weight residual False -2.31 -2.48 0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" C7 PX4 D 101 " pdb=" C6 PX4 D 101 " pdb=" C8 PX4 D 101 " pdb=" O7 PX4 D 101 " both_signs ideal model delta sigma weight residual False -2.31 -2.47 0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 926 not shown) Planarity restraints: 846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 58 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.01e+00 pdb=" C ASN B 58 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN B 58 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP B 59 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 67 " -0.010 2.00e-02 2.50e+03 1.06e-02 2.83e+00 pdb=" CG TRP J 67 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP J 67 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP J 67 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 67 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP J 67 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP J 67 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 67 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 67 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP J 67 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 75 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.16e+00 pdb=" N PRO H 76 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO H 76 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 76 " -0.020 5.00e-02 4.00e+02 ... (remaining 843 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 973 2.76 - 3.29: 5656 3.29 - 3.83: 8839 3.83 - 4.36: 9627 4.36 - 4.90: 17881 Nonbonded interactions: 42976 Sorted by model distance: nonbonded pdb=" O PHE B 140 " pdb=" OG SER B 144 " model vdw 2.222 3.040 nonbonded pdb=" O ILE D 31 " pdb=" OG SER D 34 " model vdw 2.237 3.040 nonbonded pdb=" O PHE H 140 " pdb=" OG SER H 144 " model vdw 2.241 3.040 nonbonded pdb=" O SER E 137 " pdb=" OG SER E 137 " model vdw 2.249 3.040 nonbonded pdb=" O LEU E 73 " pdb=" NH2 ARG E 108 " model vdw 2.256 3.120 ... (remaining 42971 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 101) selection = chain 'D' selection = (chain 'G' and resid 8 through 101) selection = chain 'J' } ncs_group { reference = (chain 'B' and resid 55 through 159) selection = (chain 'E' and resid 55 through 159) selection = chain 'H' selection = (chain 'K' and resid 55 through 159) } 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: 8.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.370 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.000 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5685 Z= 0.204 Angle : 0.610 9.583 7657 Z= 0.303 Chirality : 0.039 0.182 929 Planarity : 0.004 0.054 846 Dihedral : 19.830 168.845 2172 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.94 % Favored : 94.75 % Rotamer: Outliers : 0.17 % Allowed : 27.21 % Favored : 72.62 % 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 are not related in a simple way. whole: 3.09 (0.33), residues: 648 helix: 2.92 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -2.99 (0.48), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 108 TYR 0.015 0.001 TYR E 100 PHE 0.016 0.001 PHE G 11 TRP 0.029 0.002 TRP J 67 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 5685) covalent geometry : angle 0.61027 ( 7657) hydrogen bonds : bond 0.09166 ( 431) hydrogen bonds : angle 3.73839 ( 1293) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: E 133 VAL cc_start: 0.8888 (t) cc_final: 0.8678 (t) outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 0.0546 time to fit residues: 14.8992 Evaluate side-chains 110 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 GLN E 158 ASN K 113 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.045215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.037734 restraints weight = 36006.748| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 4.43 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5685 Z= 0.171 Angle : 0.629 11.986 7657 Z= 0.315 Chirality : 0.041 0.167 929 Planarity : 0.005 0.063 846 Dihedral : 19.513 165.780 1056 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.32 % Favored : 95.22 % Rotamer: Outliers : 3.57 % Allowed : 23.30 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.32), residues: 648 helix: 2.86 (0.20), residues: 536 sheet: None (None), residues: 0 loop : -2.75 (0.46), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 108 TYR 0.018 0.001 TYR H 100 PHE 0.016 0.002 PHE E 69 TRP 0.017 0.002 TRP J 67 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 5685) covalent geometry : angle 0.62905 ( 7657) hydrogen bonds : bond 0.04299 ( 431) hydrogen bonds : angle 3.71161 ( 1293) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: B 117 MET cc_start: 0.8443 (mmm) cc_final: 0.8167 (tmm) REVERT: J 66 MET cc_start: 0.7873 (tmm) cc_final: 0.7659 (ppp) outliers start: 21 outliers final: 9 residues processed: 139 average time/residue: 0.0489 time to fit residues: 9.7686 Evaluate side-chains 116 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain K residue 88 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 33 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.045714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.038483 restraints weight = 34686.444| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 4.28 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5685 Z= 0.139 Angle : 0.591 10.167 7657 Z= 0.291 Chirality : 0.040 0.154 929 Planarity : 0.004 0.042 846 Dihedral : 18.561 156.311 1056 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.63 % Favored : 94.91 % Rotamer: Outliers : 2.38 % Allowed : 21.77 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.29 (0.32), residues: 648 helix: 3.11 (0.21), residues: 532 sheet: None (None), residues: 0 loop : -2.74 (0.45), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 108 TYR 0.018 0.001 TYR E 100 PHE 0.011 0.001 PHE D 51 TRP 0.010 0.001 TRP J 67 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 5685) covalent geometry : angle 0.59115 ( 7657) hydrogen bonds : bond 0.03977 ( 431) hydrogen bonds : angle 3.56789 ( 1293) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: H 74 TYR cc_start: 0.8641 (m-80) cc_final: 0.8392 (m-80) REVERT: H 100 TYR cc_start: 0.9384 (t80) cc_final: 0.9140 (t80) outliers start: 14 outliers final: 6 residues processed: 130 average time/residue: 0.0442 time to fit residues: 8.4214 Evaluate side-chains 115 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain K residue 88 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 6 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.045707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.038599 restraints weight = 35351.328| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 4.21 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5685 Z= 0.122 Angle : 0.590 12.163 7657 Z= 0.286 Chirality : 0.040 0.161 929 Planarity : 0.004 0.035 846 Dihedral : 17.822 147.083 1056 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.48 % Favored : 95.22 % Rotamer: Outliers : 3.23 % Allowed : 22.62 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.40 (0.32), residues: 648 helix: 3.17 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -2.89 (0.45), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 108 TYR 0.012 0.001 TYR H 100 PHE 0.012 0.001 PHE D 51 TRP 0.009 0.001 TRP J 67 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 5685) covalent geometry : angle 0.58980 ( 7657) hydrogen bonds : bond 0.03760 ( 431) hydrogen bonds : angle 3.52710 ( 1293) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: B 58 ASN cc_start: 0.8793 (m-40) cc_final: 0.8483 (t0) REVERT: B 83 MET cc_start: 0.8853 (mtp) cc_final: 0.8625 (mtp) REVERT: H 100 TYR cc_start: 0.9531 (t80) cc_final: 0.9318 (t80) REVERT: K 62 THR cc_start: 0.9316 (p) cc_final: 0.9063 (p) REVERT: K 157 MET cc_start: 0.8834 (mmm) cc_final: 0.8514 (mmm) outliers start: 19 outliers final: 9 residues processed: 136 average time/residue: 0.0494 time to fit residues: 9.7172 Evaluate side-chains 121 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 88 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 5 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN ** K 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.045656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.038447 restraints weight = 36280.330| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 4.16 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5685 Z= 0.143 Angle : 0.629 12.897 7657 Z= 0.302 Chirality : 0.041 0.172 929 Planarity : 0.004 0.033 846 Dihedral : 17.604 148.762 1056 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.09 % Favored : 94.60 % Rotamer: Outliers : 3.23 % Allowed : 23.30 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.32), residues: 648 helix: 2.98 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -2.89 (0.46), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 108 TYR 0.015 0.001 TYR H 145 PHE 0.013 0.001 PHE D 51 TRP 0.009 0.001 TRP J 67 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 5685) covalent geometry : angle 0.62858 ( 7657) hydrogen bonds : bond 0.03932 ( 431) hydrogen bonds : angle 3.68641 ( 1293) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: B 58 ASN cc_start: 0.8805 (m-40) cc_final: 0.8484 (t0) REVERT: E 83 MET cc_start: 0.9148 (ptp) cc_final: 0.8866 (ptm) REVERT: H 100 TYR cc_start: 0.9536 (t80) cc_final: 0.9318 (t80) REVERT: K 108 ARG cc_start: 0.8093 (tpp80) cc_final: 0.7679 (tpp80) REVERT: K 157 MET cc_start: 0.8901 (mmm) cc_final: 0.8630 (mmm) outliers start: 19 outliers final: 13 residues processed: 130 average time/residue: 0.0465 time to fit residues: 8.6587 Evaluate side-chains 121 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 88 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 50.0000 chunk 40 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN ** K 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.045629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.038516 restraints weight = 36299.171| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 4.12 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5685 Z= 0.127 Angle : 0.647 12.798 7657 Z= 0.305 Chirality : 0.041 0.178 929 Planarity : 0.004 0.032 846 Dihedral : 17.040 145.977 1056 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.78 % Favored : 94.91 % Rotamer: Outliers : 3.06 % Allowed : 24.66 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.24 (0.32), residues: 648 helix: 3.05 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -2.84 (0.45), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 108 TYR 0.013 0.001 TYR H 145 PHE 0.015 0.001 PHE D 51 TRP 0.007 0.001 TRP J 67 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 5685) covalent geometry : angle 0.64663 ( 7657) hydrogen bonds : bond 0.03802 ( 431) hydrogen bonds : angle 3.64309 ( 1293) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: B 58 ASN cc_start: 0.8809 (m-40) cc_final: 0.8487 (t0) REVERT: B 83 MET cc_start: 0.9142 (mtp) cc_final: 0.8852 (mtp) REVERT: B 135 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.7845 (p) REVERT: H 153 PHE cc_start: 0.9520 (t80) cc_final: 0.9165 (t80) REVERT: J 49 MET cc_start: 0.9294 (mmm) cc_final: 0.8972 (mmm) REVERT: K 157 MET cc_start: 0.8872 (mmm) cc_final: 0.8614 (mmm) outliers start: 18 outliers final: 10 residues processed: 128 average time/residue: 0.0457 time to fit residues: 8.4697 Evaluate side-chains 118 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 84 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 7.9990 chunk 39 optimal weight: 30.0000 chunk 52 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.045749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.038611 restraints weight = 36965.219| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 4.15 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5685 Z= 0.130 Angle : 0.655 14.493 7657 Z= 0.312 Chirality : 0.043 0.201 929 Planarity : 0.004 0.033 846 Dihedral : 16.718 145.551 1056 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.09 % Favored : 94.60 % Rotamer: Outliers : 3.06 % Allowed : 25.34 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.24 (0.32), residues: 648 helix: 3.03 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -2.76 (0.46), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 108 TYR 0.013 0.001 TYR H 145 PHE 0.017 0.001 PHE D 51 TRP 0.007 0.001 TRP J 67 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 5685) covalent geometry : angle 0.65496 ( 7657) hydrogen bonds : bond 0.03843 ( 431) hydrogen bonds : angle 3.69116 ( 1293) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.196 Fit side-chains REVERT: B 58 ASN cc_start: 0.8836 (m-40) cc_final: 0.8534 (t0) REVERT: B 83 MET cc_start: 0.9137 (mtp) cc_final: 0.8894 (mtp) REVERT: J 49 MET cc_start: 0.9257 (mmm) cc_final: 0.9006 (mmm) REVERT: K 157 MET cc_start: 0.8909 (mmm) cc_final: 0.8650 (mmm) outliers start: 18 outliers final: 11 residues processed: 127 average time/residue: 0.0440 time to fit residues: 8.4389 Evaluate side-chains 122 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 88 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 46 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN ** K 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.045238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.038359 restraints weight = 36756.694| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.92 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5685 Z= 0.160 Angle : 0.729 14.244 7657 Z= 0.342 Chirality : 0.045 0.188 929 Planarity : 0.004 0.035 846 Dihedral : 17.001 150.131 1056 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.09 % Favored : 94.60 % Rotamer: Outliers : 3.23 % Allowed : 25.85 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.32), residues: 648 helix: 2.94 (0.20), residues: 528 sheet: None (None), residues: 0 loop : -2.99 (0.46), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 61 TYR 0.010 0.001 TYR H 145 PHE 0.021 0.001 PHE D 51 TRP 0.009 0.001 TRP J 67 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 5685) covalent geometry : angle 0.72850 ( 7657) hydrogen bonds : bond 0.04193 ( 431) hydrogen bonds : angle 3.91303 ( 1293) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: B 58 ASN cc_start: 0.8742 (m-40) cc_final: 0.8483 (t0) REVERT: B 83 MET cc_start: 0.9014 (mtp) cc_final: 0.8799 (mtp) REVERT: H 153 PHE cc_start: 0.9459 (t80) cc_final: 0.9135 (t80) REVERT: K 157 MET cc_start: 0.8863 (mmm) cc_final: 0.8647 (mmm) outliers start: 19 outliers final: 13 residues processed: 125 average time/residue: 0.0483 time to fit residues: 8.9962 Evaluate side-chains 118 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 88 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 48 optimal weight: 0.2980 chunk 23 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.045689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.038709 restraints weight = 36154.426| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 4.13 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5685 Z= 0.132 Angle : 0.713 14.994 7657 Z= 0.333 Chirality : 0.045 0.221 929 Planarity : 0.004 0.032 846 Dihedral : 16.430 145.525 1056 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.78 % Favored : 94.91 % Rotamer: Outliers : 2.21 % Allowed : 27.21 % Favored : 70.58 % 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: 3.02 (0.32), residues: 648 helix: 2.99 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -3.03 (0.45), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 61 TYR 0.013 0.001 TYR H 145 PHE 0.017 0.001 PHE D 51 TRP 0.008 0.001 TRP J 67 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5685) covalent geometry : angle 0.71253 ( 7657) hydrogen bonds : bond 0.03987 ( 431) hydrogen bonds : angle 3.87789 ( 1293) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.195 Fit side-chains REVERT: B 58 ASN cc_start: 0.8767 (m-40) cc_final: 0.8485 (t0) REVERT: B 83 MET cc_start: 0.9089 (mtp) cc_final: 0.8834 (mtp) REVERT: B 117 MET cc_start: 0.8591 (tmm) cc_final: 0.8378 (tmm) REVERT: H 153 PHE cc_start: 0.9485 (t80) cc_final: 0.9188 (t80) REVERT: K 157 MET cc_start: 0.8881 (mmm) cc_final: 0.8637 (mmm) outliers start: 13 outliers final: 11 residues processed: 125 average time/residue: 0.0468 time to fit residues: 8.7787 Evaluate side-chains 121 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 17 optimal weight: 0.0570 chunk 19 optimal weight: 40.0000 chunk 44 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.046021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.038906 restraints weight = 37211.076| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 4.21 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5685 Z= 0.137 Angle : 0.761 14.711 7657 Z= 0.349 Chirality : 0.045 0.197 929 Planarity : 0.004 0.033 846 Dihedral : 16.298 146.072 1056 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.78 % Favored : 94.91 % Rotamer: Outliers : 2.04 % Allowed : 27.38 % Favored : 70.58 % 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: 2.97 (0.32), residues: 648 helix: 2.95 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -2.97 (0.45), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 108 TYR 0.013 0.001 TYR H 145 PHE 0.025 0.001 PHE D 51 TRP 0.009 0.001 TRP J 67 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 5685) covalent geometry : angle 0.76124 ( 7657) hydrogen bonds : bond 0.04074 ( 431) hydrogen bonds : angle 3.92547 ( 1293) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.139 Fit side-chains REVERT: B 58 ASN cc_start: 0.8820 (m-40) cc_final: 0.8561 (t0) REVERT: B 83 MET cc_start: 0.9138 (mtp) cc_final: 0.8874 (mtp) REVERT: B 117 MET cc_start: 0.8648 (tmm) cc_final: 0.8420 (tmm) REVERT: H 153 PHE cc_start: 0.9528 (t80) cc_final: 0.9238 (t80) REVERT: K 157 MET cc_start: 0.8916 (mmm) cc_final: 0.8640 (mmm) outliers start: 12 outliers final: 12 residues processed: 123 average time/residue: 0.0428 time to fit residues: 7.9519 Evaluate side-chains 126 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 52 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 50.0000 chunk 58 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.045784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.038784 restraints weight = 37215.234| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 4.14 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5685 Z= 0.149 Angle : 0.747 14.465 7657 Z= 0.349 Chirality : 0.045 0.189 929 Planarity : 0.004 0.034 846 Dihedral : 16.486 148.960 1056 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.09 % Favored : 94.75 % Rotamer: Outliers : 2.38 % Allowed : 27.21 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.32), residues: 648 helix: 2.93 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -2.94 (0.46), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 61 TYR 0.011 0.001 TYR H 145 PHE 0.024 0.001 PHE D 51 TRP 0.011 0.001 TRP J 67 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 5685) covalent geometry : angle 0.74674 ( 7657) hydrogen bonds : bond 0.04110 ( 431) hydrogen bonds : angle 3.94049 ( 1293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1030.00 seconds wall clock time: 18 minutes 32.21 seconds (1112.21 seconds total)